HEADER OXIDOREDUCTASE 16-MAY-14 4PLF TITLE CRYSTAL STRUCTURE OF ANCESTRAL APICOMPLEXAN LACTATE DEHYDROGENASE WITH TITLE 2 LACTATE. COMPND MOL_ID: 1; COMPND 2 MOLECULE: LACTATE DEHYDROGENASE; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: APICOMPLEXA; SOURCE 3 ORGANISM_TAXID: 5794; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21 DE3 (PLYSS); SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID KEYWDS ANCESTRAL SEQUENCE RECONSTRUCTION, DEHYDROGENASE, APICOMPLEXA, KEYWDS 2 SPECIFICITY, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR J.I.BOUCHER,J.R.JACOBOWITZ,B.C.BECKETT,S.CLASSEN,D.L.THEOBALD REVDAT 8 15-NOV-23 4PLF 1 ATOM REVDAT 7 27-SEP-23 4PLF 1 REMARK REVDAT 6 25-DEC-19 4PLF 1 REMARK REVDAT 5 27-SEP-17 4PLF 1 SOURCE REMARK REVDAT 4 01-OCT-14 4PLF 1 JRNL REVDAT 3 24-SEP-14 4PLF 1 AUTHOR REVDAT 2 16-JUL-14 4PLF 1 JRNL REVDAT 1 02-JUL-14 4PLF 0 JRNL AUTH J.I.BOUCHER,J.R.JACOBOWITZ,B.C.BECKETT,S.CLASSEN, JRNL AUTH 2 D.L.THEOBALD JRNL TITL AN ATOMIC-RESOLUTION VIEW OF NEOFUNCTIONALIZATION IN THE JRNL TITL 2 EVOLUTION OF APICOMPLEXAN LACTATE DEHYDROGENASES. JRNL REF ELIFE V. 3 02304 2014 JRNL REFN ESSN 2050-084X JRNL PMID 24966208 JRNL DOI 10.7554/ELIFE.02304 REMARK 2 REMARK 2 RESOLUTION. 1.35 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8.4_1496) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.35 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.46 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.990 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 161482 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.121 REMARK 3 R VALUE (WORKING SET) : 0.121 REMARK 3 FREE R VALUE : 0.144 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 1.080 REMARK 3 FREE R VALUE TEST SET COUNT : 1737 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 44.4829 - 3.0909 1.00 13814 150 0.1275 0.1275 REMARK 3 2 3.0909 - 2.4534 1.00 13498 147 0.1146 0.1216 REMARK 3 3 2.4534 - 2.1433 1.00 13410 146 0.0930 0.1344 REMARK 3 4 2.1433 - 1.9473 1.00 13377 145 0.0960 0.1202 REMARK 3 5 1.9473 - 1.8077 1.00 13352 146 0.0976 0.1370 REMARK 3 6 1.8077 - 1.7011 1.00 13313 144 0.1033 0.1461 REMARK 3 7 1.7011 - 1.6159 1.00 13322 145 0.1068 0.1618 REMARK 3 8 1.6159 - 1.5456 1.00 13280 145 0.1195 0.1667 REMARK 3 9 1.5456 - 1.4861 1.00 13313 145 0.1358 0.2135 REMARK 3 10 1.4861 - 1.4348 1.00 13267 143 0.1682 0.2130 REMARK 3 11 1.4348 - 1.3899 1.00 13141 143 0.2058 0.2424 REMARK 3 12 1.3899 - 1.3500 0.95 12658 138 0.2544 0.2778 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.130 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 14.990 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 12.79 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.29 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.022 5423 REMARK 3 ANGLE : 1.897 7362 REMARK 3 CHIRALITY : 0.115 842 REMARK 3 PLANARITY : 0.012 949 REMARK 3 DIHEDRAL : 13.949 2082 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4PLF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 21-MAY-14. REMARK 100 THE DEPOSITION ID IS D_1000201621. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-SEP-12 REMARK 200 TEMPERATURE (KELVIN) : 90 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 12.3.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.115866 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 161490 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.350 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 9.500 REMARK 200 R MERGE (I) : 0.07700 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 18.2600 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.35 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.43 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.3 REMARK 200 DATA REDUNDANCY IN SHELL : 7.00 REMARK 200 R MERGE FOR SHELL (I) : 1.23000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.540 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: 1PZF REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.93 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.56 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20MG/ML PROTEIN WITH 2MM NADH/L REMARK 280 -LACTATE; WELL SOLUTION: 20% (W/V) PEG-1500, 0.1M HEPES, PH7.5, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 45.71000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 45.71000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 56.72000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 71.59500 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 56.72000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 71.59500 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 45.71000 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 56.72000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 71.59500 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 45.71000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 56.72000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 71.59500 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 22470 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 41770 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -77.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 -45.71000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 605 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 620 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 631 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 660 LIES ON A SPECIAL POSITION. REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A 1 REMARK 465 THR A 2 REMARK 465 GLY A 3 REMARK 465 THR A 4 REMARK 465 HIS A 330 REMARK 465 HIS A 331 REMARK 465 HIS A 332 REMARK 465 HIS A 333 REMARK 465 HIS A 334 REMARK 465 MET B 1 REMARK 465 THR B 2 REMARK 465 GLY B 3 REMARK 465 THR B 4 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 GLU A 328 CG CD OE1 OE2 REMARK 470 HIS A 329 CG ND1 CD2 CE1 NE2 REMARK 470 MET B 5 CG SD CE REMARK 470 LYS B 7 CE NZ REMARK 470 GLU B 142 CD OE1 OE2 REMARK 470 GLU B 220 CG CD OE1 OE2 REMARK 470 LYS B 317 CD CE NZ REMARK 470 GLU B 328 CG CD OE1 OE2 REMARK 470 HIS B 330 CG ND1 CD2 CE1 NE2 REMARK 470 HIS B 334 CG ND1 CD2 CE1 NE2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 HZ3 LYS B 88 OD1 ASP B 94 1.59 REMARK 500 O HOH B 674 O HOH B 833 1.92 REMARK 500 O HOH A 721 O HOH A 932 1.93 REMARK 500 O HOH A 598 O HOH A 624 1.93 REMARK 500 O HOH A 625 O HOH A 743 1.95 REMARK 500 O HOH A 590 O HOH A 642 1.98 REMARK 500 O HOH A 824 O HOH A 825 1.98 REMARK 500 O HOH B 879 O HOH B 883 1.98 REMARK 500 O HOH A 510 O HOH A 597 2.00 REMARK 500 O HOH B 672 O HOH B 798 2.00 REMARK 500 O HOH A 506 O HOH A 859 2.02 REMARK 500 O HOH A 1011 O HOH A 1014 2.02 REMARK 500 OE1 GLU B 254 O HOH B 834 2.03 REMARK 500 O HOH B 729 O HOH B 902 2.03 REMARK 500 O HOH B 517 O HOH B 553 2.05 REMARK 500 O HOH A 794 O HOH A 1006 2.05 REMARK 500 O HOH A 1009 O HOH A 1020 2.05 REMARK 500 O HOH A 1013 O HOH A 1016 2.06 REMARK 500 O HOH A 959 O HOH B 889 2.06 REMARK 500 O HOH B 741 O HOH B 853 2.06 REMARK 500 O HOH A 1015 O HOH B 915 2.06 REMARK 500 O HOH B 813 O HOH B 839 2.07 REMARK 500 O HOH A 773 O HOH B 833 2.09 REMARK 500 O HOH A 838 O HOH A 979 2.09 REMARK 500 O HOH A 786 O HOH A 928 2.10 REMARK 500 O HOH B 623 O HOH B 820 2.10 REMARK 500 O HOH B 596 O HOH B 872 2.10 REMARK 500 O HOH A 607 O HOH A 653 2.10 REMARK 500 O HOH B 819 O HOH B 860 2.10 REMARK 500 O HOH A 530 O HOH A 644 2.11 REMARK 500 O HOH B 897 O HOH B 914 2.12 REMARK 500 O HOH A 847 O HOH A 956 2.12 REMARK 500 O HOH A 903 O HOH A 928 2.12 REMARK 500 O HOH A 916 O HOH A 950 2.13 REMARK 500 O HOH A 952 O HOH A 991 2.13 REMARK 500 O HOH B 696 O HOH B 774 2.13 REMARK 500 OD1 ASP B 219 O HOH B 853 2.15 REMARK 500 O THR A 6 O HOH A 501 2.15 REMARK 500 O HOH A 932 O HOH B 685 2.15 REMARK 500 O HOH B 581 O HOH B 898 2.16 REMARK 500 O HOH B 535 O HOH B 596 2.17 REMARK 500 O HOH A 872 O HOH A 928 2.17 REMARK 500 O HOH A 868 O HOH A 929 2.17 REMARK 500 O HOH A 542 O HOH A 661 2.17 REMARK 500 O HOH A 925 O HOH A 983 2.17 REMARK 500 O HOH B 678 O HOH B 944 2.18 REMARK 500 O HOH A 917 O HOH A 1032 2.18 REMARK 500 O HOH B 879 O HOH B 906 2.18 REMARK 500 O HOH B 522 O HOH B 624 2.18 REMARK 500 O HOH A 863 O HOH A 914 2.18 REMARK 500 REMARK 500 THIS ENTRY HAS 53 CLOSE CONTACTS REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 501 O HOH B 543 3554 1.93 REMARK 500 O HOH A 601 O HOH A 634 4555 2.00 REMARK 500 O HOH A 505 O HOH B 511 8445 2.07 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 GLU A 169 CD GLU A 169 OE2 -0.076 REMARK 500 GLU A 254 CD GLU A 254 OE2 -0.082 REMARK 500 GLU A 297 CD GLU A 297 OE2 -0.098 REMARK 500 GLU A 299 CD GLU A 299 OE2 -0.068 REMARK 500 GLU B 306 CD GLU B 306 OE1 -0.095 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG A 212 NE - CZ - NH1 ANGL. DEV. = 4.9 DEGREES REMARK 500 ARG A 212 NE - CZ - NH2 ANGL. DEV. = -5.4 DEGREES REMARK 500 ARG B 164 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 ASP B 188 CB - CG - OD2 ANGL. DEV. = -7.3 DEGREES REMARK 500 ARG B 212 NE - CZ - NH1 ANGL. DEV. = 5.0 DEGREES REMARK 500 ARG B 212 NE - CZ - NH2 ANGL. DEV. = -3.0 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 ASN A 43 -28.49 76.61 REMARK 500 CYS A 121 60.25 -152.37 REMARK 500 ALA A 155 -55.99 -156.68 REMARK 500 TYR A 242 -28.25 -146.07 REMARK 500 GLU A 328 -97.79 151.27 REMARK 500 ASN B 43 -37.62 75.66 REMARK 500 CYS B 121 62.98 -151.72 REMARK 500 ALA B 155 -51.82 -158.97 REMARK 500 TYR B 242 -32.82 -143.49 REMARK 500 HIS B 333 -53.58 -132.72 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 HIS B 333 HIS B 334 -136.89 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 TYR A 25 0.10 SIDE CHAIN REMARK 500 TYR B 25 0.08 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 905 DISTANCE = 5.92 ANGSTROMS REMARK 525 HOH A 986 DISTANCE = 6.34 ANGSTROMS REMARK 525 HOH A 989 DISTANCE = 6.34 ANGSTROMS REMARK 525 HOH A1001 DISTANCE = 5.81 ANGSTROMS REMARK 525 HOH A1002 DISTANCE = 6.14 ANGSTROMS REMARK 525 HOH A1037 DISTANCE = 7.75 ANGSTROMS REMARK 525 HOH B 809 DISTANCE = 5.89 ANGSTROMS REMARK 525 HOH B 923 DISTANCE = 6.40 ANGSTROMS REMARK 525 HOH B 943 DISTANCE = 5.97 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NAI A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PYR A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NAD B 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PYR B 402 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4PLC RELATED DB: PDB REMARK 900 RELATED ID: 4PLG RELATED DB: PDB REMARK 900 RELATED ID: 4PLH RELATED DB: PDB REMARK 900 RELATED ID: 4PLT RELATED DB: PDB REMARK 900 RELATED ID: 4PLV RELATED DB: PDB REMARK 900 RELATED ID: 4PLW RELATED DB: PDB REMARK 900 RELATED ID: 4PLY RELATED DB: PDB REMARK 900 RELATED ID: 4PLZ RELATED DB: PDB DBREF 4PLF A 1 334 PDB 4PLF 4PLF 1 334 DBREF 4PLF B 1 334 PDB 4PLF 4PLF 1 334 SEQRES 1 A 334 MET THR GLY THR MET THR LYS ARG LYS LYS ILE SER LEU SEQRES 2 A 334 ILE GLY SER GLY MET ILE GLY GLY THR MET ALA TYR LEU SEQRES 3 A 334 CYS ALA GLN LYS GLU LEU GLY ASP VAL VAL LEU PHE ASP SEQRES 4 A 334 VAL VAL LYS ASN MET PRO GLN GLY LYS ALA LEU ASP LEU SEQRES 5 A 334 SER HIS SER SER SER ILE ALA ASP THR ASN VAL LYS VAL SEQRES 6 A 334 THR GLY THR ASN SER TYR GLU ASP ILE LYS GLY SER ASP SEQRES 7 A 334 VAL VAL ILE ILE THR ALA GLY LEU THR LYS ALA PRO GLY SEQRES 8 A 334 LYS SER ASP LYS GLU TRP SER ARG ASP ASP LEU LEU PRO SEQRES 9 A 334 PHE ASN ALA LYS ILE MET ARG GLU VAL GLY GLU ASN ILE SEQRES 10 A 334 LYS LYS TYR CYS PRO ASN ALA PHE VAL ILE VAL ILE THR SEQRES 11 A 334 ASN PRO LEU ASP VAL MET VAL LYS VAL LEU HIS GLU HIS SEQRES 12 A 334 SER GLY LEU PRO LYS ASN LYS VAL CYS GLY MET ALA GLY SEQRES 13 A 334 VAL LEU ASP SER SER ARG PHE ARG HIS PHE ILE ALA GLU SEQRES 14 A 334 LYS LEU ASN VAL SER PRO ARG ASP VAL GLN ALA MET VAL SEQRES 15 A 334 ILE GLY ALA HIS GLY ASP LYS MET VAL PRO LEU THR ARG SEQRES 16 A 334 TYR VAL THR VAL ASN GLY ILE PRO LEU GLN GLU PHE ILE SEQRES 17 A 334 LYS LYS GLY ARG ILE THR GLN GLU GLU ILE ASP GLU ILE SEQRES 18 A 334 VAL GLU ARG THR LYS ASN ALA GLY GLY GLU ILE VAL ASN SEQRES 19 A 334 LEU LEU GLY GLN GLY SER ALA TYR PHE ALA PRO ALA ALA SEQRES 20 A 334 SER ALA ILE GLU MET ALA GLU ALA TYR LEU LYS ASP LYS SEQRES 21 A 334 LYS ARG VAL LEU VAL CYS SER CYS TYR LEU GLU GLY GLN SEQRES 22 A 334 TYR GLY HIS LYS ASP MET PHE VAL GLY VAL PRO ALA VAL SEQRES 23 A 334 ILE GLY GLY ASN GLY VAL GLU LYS VAL ILE GLU LEU GLU SEQRES 24 A 334 LEU THR PRO GLU GLU LYS GLU LEU PHE ASP LYS SER VAL SEQRES 25 A 334 GLU GLU VAL ARG LYS LEU GLN LYS ALA ILE LYS ALA LEU SEQRES 26 A 334 GLY LEU GLU HIS HIS HIS HIS HIS HIS SEQRES 1 B 334 MET THR GLY THR MET THR LYS ARG LYS LYS ILE SER LEU SEQRES 2 B 334 ILE GLY SER GLY MET ILE GLY GLY THR MET ALA TYR LEU SEQRES 3 B 334 CYS ALA GLN LYS GLU LEU GLY ASP VAL VAL LEU PHE ASP SEQRES 4 B 334 VAL VAL LYS ASN MET PRO GLN GLY LYS ALA LEU ASP LEU SEQRES 5 B 334 SER HIS SER SER SER ILE ALA ASP THR ASN VAL LYS VAL SEQRES 6 B 334 THR GLY THR ASN SER TYR GLU ASP ILE LYS GLY SER ASP SEQRES 7 B 334 VAL VAL ILE ILE THR ALA GLY LEU THR LYS ALA PRO GLY SEQRES 8 B 334 LYS SER ASP LYS GLU TRP SER ARG ASP ASP LEU LEU PRO SEQRES 9 B 334 PHE ASN ALA LYS ILE MET ARG GLU VAL GLY GLU ASN ILE SEQRES 10 B 334 LYS LYS TYR CYS PRO ASN ALA PHE VAL ILE VAL ILE THR SEQRES 11 B 334 ASN PRO LEU ASP VAL MET VAL LYS VAL LEU HIS GLU HIS SEQRES 12 B 334 SER GLY LEU PRO LYS ASN LYS VAL CYS GLY MET ALA GLY SEQRES 13 B 334 VAL LEU ASP SER SER ARG PHE ARG HIS PHE ILE ALA GLU SEQRES 14 B 334 LYS LEU ASN VAL SER PRO ARG ASP VAL GLN ALA MET VAL SEQRES 15 B 334 ILE GLY ALA HIS GLY ASP LYS MET VAL PRO LEU THR ARG SEQRES 16 B 334 TYR VAL THR VAL ASN GLY ILE PRO LEU GLN GLU PHE ILE SEQRES 17 B 334 LYS LYS GLY ARG ILE THR GLN GLU GLU ILE ASP GLU ILE SEQRES 18 B 334 VAL GLU ARG THR LYS ASN ALA GLY GLY GLU ILE VAL ASN SEQRES 19 B 334 LEU LEU GLY GLN GLY SER ALA TYR PHE ALA PRO ALA ALA SEQRES 20 B 334 SER ALA ILE GLU MET ALA GLU ALA TYR LEU LYS ASP LYS SEQRES 21 B 334 LYS ARG VAL LEU VAL CYS SER CYS TYR LEU GLU GLY GLN SEQRES 22 B 334 TYR GLY HIS LYS ASP MET PHE VAL GLY VAL PRO ALA VAL SEQRES 23 B 334 ILE GLY GLY ASN GLY VAL GLU LYS VAL ILE GLU LEU GLU SEQRES 24 B 334 LEU THR PRO GLU GLU LYS GLU LEU PHE ASP LYS SER VAL SEQRES 25 B 334 GLU GLU VAL ARG LYS LEU GLN LYS ALA ILE LYS ALA LEU SEQRES 26 B 334 GLY LEU GLU HIS HIS HIS HIS HIS HIS HET NAI A 401 71 HET PYR A 402 9 HET NAD B 401 70 HET PYR B 402 9 HETNAM NAI 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE HETNAM PYR PYRUVIC ACID HETNAM NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE HETSYN NAI NADH FORMUL 3 NAI C21 H29 N7 O14 P2 FORMUL 4 PYR 2(C3 H4 O3) FORMUL 5 NAD C21 H27 N7 O14 P2 FORMUL 7 HOH *1024(H2 O) HELIX 1 AA1 GLY A 17 GLU A 31 1 15 HELIX 2 AA2 ASN A 43 ALA A 59 1 17 HELIX 3 AA3 SER A 70 LYS A 75 5 6 HELIX 4 AA4 SER A 98 ASP A 101 5 4 HELIX 5 AA5 LEU A 102 CYS A 121 1 20 HELIX 6 AA6 PRO A 132 GLY A 145 1 14 HELIX 7 AA7 PRO A 147 ASN A 149 5 3 HELIX 8 AA8 ALA A 155 ASN A 172 1 18 HELIX 9 AA9 SER A 174 ARG A 176 5 3 HELIX 10 AB1 THR A 194 TYR A 196 5 3 HELIX 11 AB2 LEU A 204 LYS A 210 1 7 HELIX 12 AB3 THR A 214 GLY A 237 1 24 HELIX 13 AB4 TYR A 242 LYS A 258 1 17 HELIX 14 AB5 GLN A 273 GLY A 275 5 3 HELIX 15 AB6 THR A 301 LEU A 325 1 25 HELIX 16 AB7 GLY B 17 GLU B 31 1 15 HELIX 17 AB8 ASN B 43 ALA B 59 1 17 HELIX 18 AB9 SER B 70 LYS B 75 5 6 HELIX 19 AC1 SER B 98 ASP B 101 5 4 HELIX 20 AC2 LEU B 102 CYS B 121 1 20 HELIX 21 AC3 PRO B 132 GLY B 145 1 14 HELIX 22 AC4 PRO B 147 ASN B 149 5 3 HELIX 23 AC5 ALA B 155 ASN B 172 1 18 HELIX 24 AC6 SER B 174 ARG B 176 5 3 HELIX 25 AC7 THR B 194 TYR B 196 5 3 HELIX 26 AC8 LEU B 204 LYS B 210 1 7 HELIX 27 AC9 THR B 214 GLY B 237 1 24 HELIX 28 AD1 TYR B 242 LYS B 258 1 17 HELIX 29 AD2 GLN B 273 GLY B 275 5 3 HELIX 30 AD3 THR B 301 GLY B 326 1 26 SHEET 1 AA1 6 VAL A 65 THR A 68 0 SHEET 2 AA1 6 ASP A 34 PHE A 38 1 N LEU A 37 O THR A 66 SHEET 3 AA1 6 LYS A 10 ILE A 14 1 N LEU A 13 O VAL A 36 SHEET 4 AA1 6 VAL A 79 ILE A 82 1 O VAL A 79 N SER A 12 SHEET 5 AA1 6 PHE A 125 VAL A 128 1 O ILE A 127 N ILE A 82 SHEET 6 AA1 6 VAL A 151 GLY A 153 1 O CYS A 152 N VAL A 128 SHEET 1 AA2 3 VAL A 178 GLN A 179 0 SHEET 2 AA2 3 THR A 198 VAL A 199 -1 O THR A 198 N GLN A 179 SHEET 3 AA2 3 ILE A 202 PRO A 203 -1 O ILE A 202 N VAL A 199 SHEET 1 AA3 2 VAL A 182 ILE A 183 0 SHEET 2 AA3 2 VAL A 191 PRO A 192 -1 O VAL A 191 N ILE A 183 SHEET 1 AA4 3 ARG A 262 GLU A 271 0 SHEET 2 AA4 3 LYS A 277 GLY A 288 -1 O ASP A 278 N LEU A 270 SHEET 3 AA4 3 GLY A 291 VAL A 295 -1 O LYS A 294 N VAL A 286 SHEET 1 AA5 6 VAL B 65 THR B 68 0 SHEET 2 AA5 6 ASP B 34 PHE B 38 1 N LEU B 37 O THR B 66 SHEET 3 AA5 6 LYS B 10 ILE B 14 1 N LEU B 13 O VAL B 36 SHEET 4 AA5 6 VAL B 79 ILE B 82 1 O ILE B 81 N SER B 12 SHEET 5 AA5 6 PHE B 125 VAL B 128 1 O ILE B 127 N ILE B 82 SHEET 6 AA5 6 VAL B 151 GLY B 153 1 O CYS B 152 N VAL B 128 SHEET 1 AA6 3 VAL B 178 GLN B 179 0 SHEET 2 AA6 3 THR B 198 VAL B 199 -1 O THR B 198 N GLN B 179 SHEET 3 AA6 3 ILE B 202 PRO B 203 -1 O ILE B 202 N VAL B 199 SHEET 1 AA7 2 VAL B 182 ILE B 183 0 SHEET 2 AA7 2 VAL B 191 PRO B 192 -1 O VAL B 191 N ILE B 183 SHEET 1 AA8 3 ARG B 262 GLU B 271 0 SHEET 2 AA8 3 LYS B 277 GLY B 288 -1 O ILE B 287 N ARG B 262 SHEET 3 AA8 3 GLY B 291 VAL B 295 -1 O GLU B 293 N VAL B 286 CISPEP 1 ASN A 131 PRO A 132 0 -6.61 CISPEP 2 ASN B 131 PRO B 132 0 -5.04 SITE 1 AC1 35 GLY A 17 MET A 18 ILE A 19 PHE A 38 SITE 2 AC1 35 ASP A 39 VAL A 40 VAL A 41 MET A 44 SITE 3 AC1 35 THR A 83 ALA A 84 GLY A 85 LEU A 86 SITE 4 AC1 35 THR A 87 ASN A 106 ILE A 109 ILE A 129 SITE 5 AC1 35 ASN A 131 MET A 154 LEU A 158 HIS A 186 SITE 6 AC1 35 ALA A 241 PRO A 245 PYR A 402 HOH A 531 SITE 7 AC1 35 HOH A 536 HOH A 675 HOH A 682 HOH A 690 SITE 8 AC1 35 HOH A 694 HOH A 755 HOH A 766 HOH A 818 SITE 9 AC1 35 HOH A 836 HOH A 917 HOH A1054 SITE 1 AC2 7 ARG A 99 ASN A 131 ARG A 162 HIS A 186 SITE 2 AC2 7 GLY A 229 NAI A 401 HOH A 680 SITE 1 AC3 34 GLY B 17 MET B 18 ILE B 19 PHE B 38 SITE 2 AC3 34 ASP B 39 VAL B 40 VAL B 41 TYR B 71 SITE 3 AC3 34 THR B 83 ALA B 84 GLY B 85 LEU B 86 SITE 4 AC3 34 THR B 87 LEU B 102 ASN B 106 ILE B 109 SITE 5 AC3 34 ILE B 129 THR B 130 ASN B 131 MET B 154 SITE 6 AC3 34 LEU B 158 HIS B 186 PYR B 402 HOH B 633 SITE 7 AC3 34 HOH B 672 HOH B 707 HOH B 721 HOH B 737 SITE 8 AC3 34 HOH B 744 HOH B 751 HOH B 775 HOH B 798 SITE 9 AC3 34 HOH B 828 HOH B 931 SITE 1 AC4 8 TRP B 97 ARG B 99 ASN B 131 ARG B 162 SITE 2 AC4 8 HIS B 186 GLY B 229 NAD B 401 HOH B 653 CRYST1 113.440 143.190 91.420 90.00 90.00 90.00 C 2 2 21 16 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.008815 0.000000 0.000000 0.00000 SCALE2 0.000000 0.006984 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010939 0.00000