HEADER LYASE 28-APR-16 5JMF TITLE HEPARINASE III-BT4657 GENE PRODUCT COMPND MOL_ID: 1; COMPND 2 MOLECULE: HEPARINASE III PROTEIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACTEROIDES THETAIOTAOMICRON; SOURCE 3 ORGANISM_TAXID: 226186; SOURCE 4 STRAIN: ATCC 29148 / DSM 2079 / NCTC 10582 / E50 / VPI-5482; SOURCE 5 GENE: BT_4657; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) KEYWDS HEPARINASEIII, BT4657 GENE PRODUCT, BACTEROIDES THETAIOTAOMICRON, KEYWDS 2 LYASE EXPDTA X-RAY DIFFRACTION AUTHOR T.S.ULAGANATHAN,R.SHI,D.YAO,M.-L.GARRON,M.CHERNEY,M.CYGLER REVDAT 5 17-JAN-18 5JMF 1 REMARK REVDAT 4 09-AUG-17 5JMF 1 REMARK REVDAT 3 18-JAN-17 5JMF 1 JRNL REVDAT 2 28-SEP-16 5JMF 1 JRNL REVDAT 1 25-MAY-16 5JMF 0 JRNL AUTH T.ULAGANATHAN,R.SHI,D.YAO,R.X.GU,M.L.GARRON,M.CHERNEY, JRNL AUTH 2 D.P.TIELEMAN,E.STERNER,G.LI,L.LI,R.J.LINHARDT,M.CYGLER JRNL TITL CONFORMATIONAL FLEXIBILITY OF PL12 FAMILY HEPARINASES: JRNL TITL 2 STRUCTURE AND SUBSTRATE SPECIFICITY OF HEPARINASE III FROM JRNL TITL 3 BACTEROIDES THETAIOTAOMICRON (BT4657). JRNL REF GLYCOBIOLOGY V. 27 176 2017 JRNL REFN ESSN 1460-2423 JRNL PMID 27621378 JRNL DOI 10.1093/GLYCOB/CWW096 REMARK 2 REMARK 2 RESOLUTION. 1.85 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.10.1_2155: ???) 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.85 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.50 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 3 NUMBER OF REFLECTIONS : 57221 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.167 REMARK 3 R VALUE (WORKING SET) : 0.165 REMARK 3 FREE R VALUE : 0.203 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.070 REMARK 3 FREE R VALUE TEST SET COUNT : 2903 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 20.5041 - 5.0904 0.97 2658 149 0.1645 0.1910 REMARK 3 2 5.0904 - 4.0506 1.00 2714 108 0.1299 0.1553 REMARK 3 3 4.0506 - 3.5416 1.00 2627 159 0.1425 0.1697 REMARK 3 4 3.5416 - 3.2191 1.00 2618 149 0.1514 0.1869 REMARK 3 5 3.2191 - 2.9891 1.00 2626 159 0.1639 0.2001 REMARK 3 6 2.9891 - 2.8134 1.00 2634 130 0.1749 0.1998 REMARK 3 7 2.8134 - 2.6728 1.00 2600 155 0.1717 0.2147 REMARK 3 8 2.6728 - 2.5566 1.00 2632 136 0.1823 0.2387 REMARK 3 9 2.5566 - 2.4584 1.00 2609 148 0.1814 0.2539 REMARK 3 10 2.4584 - 2.3737 1.00 2597 119 0.1897 0.2610 REMARK 3 11 2.3737 - 2.2996 1.00 2600 158 0.1611 0.2203 REMARK 3 12 2.2996 - 2.2339 0.99 2587 146 0.1708 0.1946 REMARK 3 13 2.2339 - 2.1752 0.99 2564 134 0.1655 0.2241 REMARK 3 14 2.1752 - 2.1222 0.99 2592 150 0.1726 0.2368 REMARK 3 15 2.1222 - 2.0740 0.99 2568 134 0.1851 0.2299 REMARK 3 16 2.0740 - 2.0299 0.99 2601 124 0.1920 0.2604 REMARK 3 17 2.0299 - 1.9893 0.98 2522 129 0.1987 0.2740 REMARK 3 18 1.9893 - 1.9518 0.99 2590 146 0.2128 0.2543 REMARK 3 19 1.9518 - 1.9170 0.98 2523 127 0.2191 0.2642 REMARK 3 20 1.9170 - 1.8845 0.98 2570 123 0.2319 0.2646 REMARK 3 21 1.8845 - 1.8541 0.89 2286 120 0.2510 0.2520 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.180 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.320 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 : 0.010 5441 REMARK 3 ANGLE : 0.983 7378 REMARK 3 CHIRALITY : 0.060 744 REMARK 3 PLANARITY : 0.007 953 REMARK 3 DIHEDRAL : 13.067 3175 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 21 THROUGH 245 ) REMARK 3 ORIGIN FOR THE GROUP (A): 28.2151 18.8914 64.4618 REMARK 3 T TENSOR REMARK 3 T11: 0.4391 T22: 0.3799 REMARK 3 T33: 0.4029 T12: 0.0125 REMARK 3 T13: -0.0188 T23: 0.1685 REMARK 3 L TENSOR REMARK 3 L11: 2.7605 L22: 2.2301 REMARK 3 L33: 2.0468 L12: 0.1942 REMARK 3 L13: 0.3655 L23: 0.5511 REMARK 3 S TENSOR REMARK 3 S11: 0.2049 S12: -0.7632 S13: -0.6707 REMARK 3 S21: 0.5739 S22: 0.0622 S23: -0.1233 REMARK 3 S31: 0.5888 S32: -0.0621 S33: -0.1494 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 246 THROUGH 395 ) REMARK 3 ORIGIN FOR THE GROUP (A): 52.7536 24.9916 51.7444 REMARK 3 T TENSOR REMARK 3 T11: 0.2159 T22: 0.2397 REMARK 3 T33: 0.2440 T12: 0.0128 REMARK 3 T13: -0.0018 T23: -0.0465 REMARK 3 L TENSOR REMARK 3 L11: 4.1107 L22: 0.3389 REMARK 3 L33: -0.2944 L12: -1.8531 REMARK 3 L13: -0.6711 L23: -0.1535 REMARK 3 S TENSOR REMARK 3 S11: -0.0773 S12: -0.0384 S13: 0.0567 REMARK 3 S21: 0.0647 S22: 0.0347 S23: 0.0277 REMARK 3 S31: -0.0549 S32: -0.0347 S33: 0.0318 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 396 THROUGH 666 ) REMARK 3 ORIGIN FOR THE GROUP (A): 82.8900 21.4059 61.1693 REMARK 3 T TENSOR REMARK 3 T11: 0.1579 T22: 0.1929 REMARK 3 T33: 0.1784 T12: -0.0017 REMARK 3 T13: -0.0027 T23: -0.0099 REMARK 3 L TENSOR REMARK 3 L11: 2.8941 L22: 1.8599 REMARK 3 L33: 2.0017 L12: -0.3494 REMARK 3 L13: 0.7913 L23: 0.0447 REMARK 3 S TENSOR REMARK 3 S11: -0.0803 S12: -0.2878 S13: 0.1108 REMARK 3 S21: 0.2448 S22: -0.0205 S23: -0.1843 REMARK 3 S31: -0.0684 S32: 0.0146 S33: 0.0664 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 5JMF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 29-APR-16. REMARK 100 THE DEPOSITION ID IS D_1000220876. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-MAY-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : CLSI REMARK 200 BEAMLINE : 08ID-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9796 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX-300 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 58055 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.850 REMARK 200 RESOLUTION RANGE LOW (A) : 20.503 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 200 DATA REDUNDANCY : 3.600 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 27.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.12 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.28 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG 3350, 100MM BIS-TRIS PH 5.5, REMARK 280 200MM MAGNESIUM CHLORIDE,500MM NDSB-201 AS ADDITIVE INN REMARK 280 CRYSTALLIZATION DROP, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 293.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z REMARK 290 4555 -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 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 93.34500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 22.87050 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 93.34500 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 22.87050 REMARK 290 SMTRY3 4 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 390 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 27830 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 1.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 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 A1202 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 SER A 12 REMARK 465 ASP A 13 REMARK 465 SER A 14 REMARK 465 GLU A 15 REMARK 465 ASN A 16 REMARK 465 LEU A 17 REMARK 465 TYR A 18 REMARK 465 PHE A 19 REMARK 465 GLN A 20 REMARK 465 VAL A 99 REMARK 465 HIS A 100 REMARK 465 LYS A 101 REMARK 465 GLY A 102 REMARK 465 TYR A 103 REMARK 465 GLN A 104 REMARK 465 PRO A 105 REMARK 465 SER A 106 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 LEU A 93 CG CD1 CD2 REMARK 470 LYS A 94 CG CD CE NZ REMARK 470 PHE A 98 CG CD1 CD2 CE1 CE2 CZ REMARK 470 GLU A 111 CG CD OE1 OE2 REMARK 470 GLN A 116 CG CD OE1 NE2 REMARK 470 TYR A 117 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 TRP A 118 CG CD1 CD2 NE1 CE2 CE3 CZ2 REMARK 470 TRP A 118 CZ3 CH2 REMARK 470 LYS A 121 CG CD CE NZ REMARK 470 GLN A 128 CG CD OE1 NE2 REMARK 470 LYS A 169 CD CE NZ REMARK 470 LYS A 172 CG CD CE NZ REMARK 470 LYS A 173 CG CD CE NZ REMARK 470 GLU A 176 CG CD OE1 OE2 REMARK 470 LYS A 182 CG CD CE NZ REMARK 470 ASP A 244 CG OD1 OD2 REMARK 470 GLN A 245 CG CD OE1 NE2 REMARK 470 GLU A 460 CG CD OE1 OE2 REMARK 470 GLU A 462 CG CD OE1 OE2 REMARK 470 LYS A 551 CD CE NZ REMARK 470 LYS A 598 CD CE NZ REMARK 470 LYS A 640 CD CE NZ REMARK 470 LYS A 642 CG CD CE NZ REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 LYS A 83 CG CD CE NZ REMARK 480 LYS A 149 CG CD CE NZ REMARK 480 SER A 179 OG REMARK 480 LYS A 516 CE NZ REMARK 480 LYS A 640 CG REMARK 480 GLU A 646 CD OE1 OE2 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 O HOH A 802 O HOH A 1174 2.03 REMARK 500 O HOH A 959 O HOH A 1201 2.13 REMARK 500 O LEU A 666 O HOH A 801 2.15 REMARK 500 NE2 GLN A 466 O HOH A 802 2.16 REMARK 500 O HOH A 968 O HOH A 1263 2.16 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 1099 O HOH A 1108 4546 2.12 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 THR A 67 C - N - CA ANGL. DEV. = 15.3 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 THR A 67 -88.79 138.49 REMARK 500 CYS A 352 48.27 -91.04 REMARK 500 SER A 354 -128.99 61.12 REMARK 500 ASP A 395 42.48 -85.20 REMARK 500 MET A 397 -92.00 -115.35 REMARK 500 ALA A 424 87.75 -154.19 REMARK 500 PHE A 429 -134.55 -134.98 REMARK 500 TYR A 455 -66.70 69.73 REMARK 500 ASN A 483 18.60 57.45 REMARK 500 GLU A 490 76.36 -160.20 REMARK 500 THR A 527 -54.10 -128.91 REMARK 500 ASN A 613 -169.01 -168.71 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 703 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLN A 433 OE1 REMARK 620 2 ASP A 451 OD1 169.6 REMARK 620 3 HOH A 862 O 90.6 79.1 REMARK 620 4 HOH A 885 O 90.8 88.5 90.8 REMARK 620 5 HOH A 891 O 94.4 86.7 91.1 174.4 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 701 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue TRS A 702 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 703 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5JMF RELATED DB: PDB DBREF 5JMF A 23 666 UNP Q89YS4 Q89YS4_BACTN 23 666 SEQADV 5JMF SER A 12 UNP Q89YS4 EXPRESSION TAG SEQADV 5JMF ASP A 13 UNP Q89YS4 EXPRESSION TAG SEQADV 5JMF SER A 14 UNP Q89YS4 EXPRESSION TAG SEQADV 5JMF GLU A 15 UNP Q89YS4 EXPRESSION TAG SEQADV 5JMF ASN A 16 UNP Q89YS4 EXPRESSION TAG SEQADV 5JMF LEU A 17 UNP Q89YS4 EXPRESSION TAG SEQADV 5JMF TYR A 18 UNP Q89YS4 EXPRESSION TAG SEQADV 5JMF PHE A 19 UNP Q89YS4 EXPRESSION TAG SEQADV 5JMF GLN A 20 UNP Q89YS4 EXPRESSION TAG SEQADV 5JMF GLY A 21 UNP Q89YS4 EXPRESSION TAG SEQADV 5JMF SER A 22 UNP Q89YS4 EXPRESSION TAG SEQRES 1 A 655 SER ASP SER GLU ASN LEU TYR PHE GLN GLY SER GLN GLU SEQRES 2 A 655 LEU MLY SER GLU VAL PHE SER LEU LEU ASN LEU ASP TYR SEQRES 3 A 655 PRO GLY LEU GLU LYS VAL MLY ALA LEU HIS GLN GLU GLY SEQRES 4 A 655 LYS ASP GLU ASP ALA ALA MLY ALA LEU LEU ASP TYR TYR SEQRES 5 A 655 ARG ALA ARG THR ASN VAL LYS THR PRO ASP ILE ASN LEU SEQRES 6 A 655 LYS LYS ILE THR ILE GLY LYS GLU GLU GLN GLN TRP ALA SEQRES 7 A 655 ASP ASP GLY LEU LYS HIS THR PHE PHE VAL HIS LYS GLY SEQRES 8 A 655 TYR GLN PRO SER TYR ASN TYR GLY GLU ASP ILE ASN TRP SEQRES 9 A 655 GLN TYR TRP PRO VAL LYS ASP ASN GLU LEU ARG TRP GLN SEQRES 10 A 655 LEU HIS ARG HIS LYS TRP PHE THR PRO MET GLY MLY ALA SEQRES 11 A 655 TYR ARG VAL SER GLY ASP GLU LYS TYR ALA LYS GLU TRP SEQRES 12 A 655 ALA TYR GLN TYR ILE ASP TRP ILE LYS LYS ASN PRO LEU SEQRES 13 A 655 VAL LYS MET ASP LYS LYS GLU TYR GLU LEU VAL SER ASP SEQRES 14 A 655 GLY LYS ILE LYS GLY GLU VAL GLU ASN VAL ARG PHE ALA SEQRES 15 A 655 TRP ARG PRO LEU GLU VAL SER ASN ARG LEU GLN ASP GLN SEQRES 16 A 655 THR THR GLN PHE GLN LEU PHE LEU PRO SER PRO SER PHE SEQRES 17 A 655 THR PRO ASP PHE LEU THR GLU PHE LEU VAL ASN TYR HIS SEQRES 18 A 655 LYS HIS ALA VAL HIS ILE LEU ALA ASN TYR SER ASP GLN SEQRES 19 A 655 GLY ASN HIS LEU LEU PHE GLU ALA GLN ARG MET ILE TYR SEQRES 20 A 655 ALA GLY ALA PHE PHE PRO GLU PHE MLY GLU ALA PRO ALA SEQRES 21 A 655 TRP ARG MLY SER GLY ILE ASP ILE LEU ASN ARG GLU VAL SEQRES 22 A 655 ASN VAL GLN VAL TYR ASN ASP GLY GLY GLN PHE GLU LEU SEQRES 23 A 655 ASP PRO HIS TYR HIS LEU ALA ALA ILE ASN ILE PHE CYS SEQRES 24 A 655 MLY ALA LEU GLY ILE ALA ASP VAL ASN GLY PHE ARG ASN SEQRES 25 A 655 GLU PHE PRO GLN GLU TYR LEU ASP THR ILE GLU MLY MET SEQRES 26 A 655 ILE MET PHE TYR ALA ASN ILE SER PHE PRO ASP TYR THR SEQRES 27 A 655 ASN PRO CYS PHE SER ASP ALA LYS ILE THR GLU MLY LYS SEQRES 28 A 655 GLU MET LEU LYS ASN TYR ARG ALA TRP SER LYS LEU PHE SEQRES 29 A 655 PRO MLY ASN GLU THR ILE MLY TYR LEU ALA THR ASP GLY SEQRES 30 A 655 MLY GLU GLY ALA LEU PRO ASP TYR MET SER MLY GLY PHE SEQRES 31 A 655 LEU LYS SER GLY PHE PHE VAL PHE ARG ASN SER TRP GLY SEQRES 32 A 655 MET ASP ALA THR GLN MET VAL VAL LYS ALA GLY PRO LYS SEQRES 33 A 655 GLY PHE TRP HIS CYS GLN PRO ASP ASN GLY THR PHE GLU SEQRES 34 A 655 MET TRP PHE ASN GLY LYS ASN LEU PHE PRO ASP SER GLY SEQRES 35 A 655 SER TYR VAL TYR ALA GLY GLU GLY GLU VAL MET GLU GLN SEQRES 36 A 655 ARG ASN TRP HIS ARG GLN THR SER VAL HIS ASN THR VAL SEQRES 37 A 655 THR LEU ASP ASN MLY ASN LEU GLU THR THR GLU SER VAL SEQRES 38 A 655 THR MLY LEU TRP GLN PRO GLU GLY ASN ILE GLN THR LEU SEQRES 39 A 655 VAL THR GLU ASN PRO SER TYR LYS ASN PHE LYS HIS ARG SEQRES 40 A 655 ARG SER VAL PHE PHE VAL ASP ASN THR TYR PHE VAL ILE SEQRES 41 A 655 VAL ASP GLU VAL SER GLY SER ALA MLY GLY SER VAL ASN SEQRES 42 A 655 LEU HIS TYR GLN MET PRO LYS GLY GLU ILE ALA ASN SER SEQRES 43 A 655 ARG GLU ASP MET THR PHE LEU THR GLN PHE GLU ASP GLY SEQRES 44 A 655 SER ASN MET MLY LEU GLN CYS PHE GLY PRO GLU GLY MET SEQRES 45 A 655 SER MET LYS MLY GLU PRO GLY TRP CYS SER THR ALA TYR SEQRES 46 A 655 ARG LYS ARG TYR LYS ARG MET ASN VAL SER PHE ASN VAL SEQRES 47 A 655 MLY LYS ASP ASN GLU ASN ALA VAL ARG TYR ILE THR VAL SEQRES 48 A 655 ILE TYR PRO VAL MLY MLY SER ALA ASP ALA PRO MLY PHE SEQRES 49 A 655 ASP ALA LYS PHE LYS ASN LYS THR PHE ASP GLU ASN GLY SEQRES 50 A 655 LEU GLU ILE GLU VAL MLY VAL ASN GLY MLY LYS GLN SER SEQRES 51 A 655 LEU MLY TYR LYS LEU MODRES 5JMF MLY A 26 LYS MODIFIED RESIDUE MODRES 5JMF MLY A 44 LYS MODIFIED RESIDUE MODRES 5JMF MLY A 57 LYS MODIFIED RESIDUE MODRES 5JMF MLY A 140 LYS MODIFIED RESIDUE MODRES 5JMF MLY A 267 LYS MODIFIED RESIDUE MODRES 5JMF MLY A 274 LYS MODIFIED RESIDUE MODRES 5JMF MLY A 311 LYS MODIFIED RESIDUE MODRES 5JMF MLY A 335 LYS MODIFIED RESIDUE MODRES 5JMF MLY A 361 LYS MODIFIED RESIDUE MODRES 5JMF MLY A 377 LYS MODIFIED RESIDUE MODRES 5JMF MLY A 382 LYS MODIFIED RESIDUE MODRES 5JMF MLY A 389 LYS MODIFIED RESIDUE MODRES 5JMF MLY A 399 LYS MODIFIED RESIDUE MODRES 5JMF MLY A 484 LYS MODIFIED RESIDUE MODRES 5JMF MLY A 494 LYS MODIFIED RESIDUE MODRES 5JMF MLY A 540 LYS MODIFIED RESIDUE MODRES 5JMF MLY A 574 LYS MODIFIED RESIDUE MODRES 5JMF MLY A 587 LYS MODIFIED RESIDUE MODRES 5JMF MLY A 610 LYS MODIFIED RESIDUE MODRES 5JMF MLY A 627 LYS MODIFIED RESIDUE MODRES 5JMF MLY A 628 LYS MODIFIED RESIDUE MODRES 5JMF MLY A 634 LYS MODIFIED RESIDUE MODRES 5JMF MLY A 654 LYS MODIFIED RESIDUE MODRES 5JMF MLY A 658 LYS MODIFIED RESIDUE MODRES 5JMF MLY A 663 LYS MODIFIED RESIDUE HET MLY A 26 11 HET MLY A 44 11 HET MLY A 57 11 HET MLY A 140 11 HET MLY A 267 11 HET MLY A 274 11 HET MLY A 311 11 HET MLY A 335 11 HET MLY A 361 11 HET MLY A 377 11 HET MLY A 382 11 HET MLY A 389 11 HET MLY A 399 11 HET MLY A 484 11 HET MLY A 494 11 HET MLY A 540 11 HET MLY A 574 11 HET MLY A 587 11 HET MLY A 610 11 HET MLY A 627 11 HET MLY A 628 11 HET MLY A 634 11 HET MLY A 654 11 HET MLY A 658 11 HET MLY A 663 11 HET GOL A 701 6 HET TRS A 702 8 HET MG A 703 1 HETNAM MLY N-DIMETHYL-LYSINE HETNAM GOL GLYCEROL HETNAM TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL HETNAM MG MAGNESIUM ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL HETSYN TRS TRIS BUFFER FORMUL 1 MLY 25(C8 H18 N2 O2) FORMUL 2 GOL C3 H8 O3 FORMUL 3 TRS C4 H12 N O3 1+ FORMUL 4 MG MG 2+ FORMUL 5 HOH *536(H2 O) HELIX 1 AA1 GLU A 28 LEU A 33 1 6 HELIX 2 AA2 LEU A 40 GLU A 49 1 10 HELIX 3 AA3 LYS A 51 ARG A 66 1 16 HELIX 4 AA4 GLY A 82 LYS A 94 1 13 HELIX 5 AA5 ASP A 122 HIS A 130 1 9 HELIX 6 AA6 TRP A 134 GLY A 146 1 13 HELIX 7 AA7 GLU A 148 ASN A 165 1 18 HELIX 8 AA8 ASP A 171 GLU A 176 1 6 HELIX 9 AA9 GLY A 181 TRP A 194 1 14 HELIX 10 AB1 ARG A 195 LEU A 214 1 20 HELIX 11 AB2 THR A 220 ASN A 241 1 22 HELIX 12 AB3 GLY A 246 PHE A 263 1 18 HELIX 13 AB4 GLU A 268 VAL A 288 1 21 HELIX 14 AB5 ASP A 298 VAL A 318 1 21 HELIX 15 AB6 ASN A 319 GLY A 320 5 2 HELIX 16 AB7 PHE A 321 PHE A 325 5 5 HELIX 17 AB8 PRO A 326 SER A 344 1 19 HELIX 18 AB9 GLU A 360 PHE A 375 1 16 HELIX 19 AC1 ASN A 378 THR A 386 1 9 HELIX 20 AC2 GLY A 461 GLN A 472 1 12 HELIX 21 AC3 THR A 473 HIS A 476 5 4 HELIX 22 AC4 MLY A 628 ALA A 632 5 5 SHEET 1 AA1 5 MLY A 399 PHE A 401 0 SHEET 2 AA1 5 PHE A 406 ARG A 410 -1 O VAL A 408 N MLY A 399 SHEET 3 AA1 5 THR A 418 LYS A 423 -1 O VAL A 422 N PHE A 407 SHEET 4 AA1 5 PHE A 439 PHE A 443 -1 O TRP A 442 N GLN A 419 SHEET 5 AA1 5 LYS A 446 ASN A 447 -1 O LYS A 446 N PHE A 443 SHEET 1 AA2 4 VAL A 479 LEU A 481 0 SHEET 2 AA2 4 GLY A 541 GLN A 548 -1 O ASN A 544 N THR A 480 SHEET 3 AA2 4 LYS A 598 LYS A 611 -1 O LYS A 611 N GLY A 541 SHEET 4 AA2 4 SER A 584 ALA A 595 -1 N GLU A 588 O ASN A 604 SHEET 1 AA3 8 VAL A 492 GLN A 497 0 SHEET 2 AA3 8 ILE A 502 TYR A 512 -1 O GLU A 508 N VAL A 492 SHEET 3 AA3 8 PHE A 515 VAL A 524 -1 O ARG A 519 N THR A 507 SHEET 4 AA3 8 TYR A 528 SER A 536 -1 O GLU A 534 N ARG A 518 SHEET 5 AA3 8 VAL A 617 VAL A 626 -1 O VAL A 617 N VAL A 535 SHEET 6 AA3 8 ASN A 572 PHE A 578 -1 N PHE A 578 O ILE A 620 SHEET 7 AA3 8 THR A 562 THR A 565 -1 N PHE A 563 O LEU A 575 SHEET 8 AA3 8 ILE A 554 SER A 557 -1 N ALA A 555 O LEU A 564 SHEET 1 AA4 3 PHE A 635 PHE A 639 0 SHEET 2 AA4 3 GLY A 648 VAL A 655 -1 O GLU A 652 N LYS A 638 SHEET 3 AA4 3 MLY A 658 LYS A 665 -1 O LEU A 662 N ILE A 651 LINK C LEU A 25 N MLY A 26 1555 1555 1.33 LINK C MLY A 26 N SER A 27 1555 1555 1.33 LINK C VAL A 43 N MLY A 44 1555 1555 1.33 LINK C MLY A 44 N ALA A 45 1555 1555 1.33 LINK C ALA A 56 N MLY A 57 1555 1555 1.33 LINK C MLY A 57 N ALA A 58 1555 1555 1.33 LINK C GLY A 139 N MLY A 140 1555 1555 1.33 LINK C MLY A 140 N ALA A 141 1555 1555 1.33 LINK C PHE A 266 N MLY A 267 1555 1555 1.34 LINK C MLY A 267 N GLU A 268 1555 1555 1.32 LINK C ARG A 273 N MLY A 274 1555 1555 1.34 LINK C MLY A 274 N SER A 275 1555 1555 1.33 LINK C CYS A 310 N MLY A 311 1555 1555 1.33 LINK C MLY A 311 N ALA A 312 1555 1555 1.33 LINK C GLU A 334 N MLY A 335 1555 1555 1.33 LINK C MLY A 335 N MET A 336 1555 1555 1.34 LINK C GLU A 360 N MLY A 361 1555 1555 1.33 LINK C MLY A 361 N LYS A 362 1555 1555 1.33 LINK C PRO A 376 N MLY A 377 1555 1555 1.33 LINK C MLY A 377 N ASN A 378 1555 1555 1.34 LINK C ILE A 381 N MLY A 382 1555 1555 1.34 LINK C MLY A 382 N TYR A 383 1555 1555 1.34 LINK C GLY A 388 N MLY A 389 1555 1555 1.34 LINK C MLY A 389 N GLU A 390 1555 1555 1.33 LINK C SER A 398 N MLY A 399 1555 1555 1.33 LINK C MLY A 399 N GLY A 400 1555 1555 1.33 LINK OE1 GLN A 433 MG MG A 703 1555 1555 2.04 LINK OD1 ASP A 451 MG MG A 703 1555 1555 2.22 LINK C ASN A 483 N MLY A 484 1555 1555 1.33 LINK C MLY A 484 N ASN A 485 1555 1555 1.34 LINK C THR A 493 N MLY A 494 1555 1555 1.35 LINK C MLY A 494 N LEU A 495 1555 1555 1.33 LINK C ALA A 539 N MLY A 540 1555 1555 1.33 LINK C MLY A 540 N GLY A 541 1555 1555 1.33 LINK C MET A 573 N MLY A 574 1555 1555 1.33 LINK C MLY A 574 N LEU A 575 1555 1555 1.33 LINK C LYS A 586 N MLY A 587 1555 1555 1.33 LINK C MLY A 587 N GLU A 588 1555 1555 1.33 LINK C VAL A 609 N MLY A 610 1555 1555 1.33 LINK C MLY A 610 N LYS A 611 1555 1555 1.33 LINK C VAL A 626 N MLY A 627 1555 1555 1.32 LINK C MLY A 627 N MLY A 628 1555 1555 1.34 LINK C MLY A 628 N SER A 629 1555 1555 1.34 LINK C PRO A 633 N MLY A 634 1555 1555 1.33 LINK C MLY A 634 N PHE A 635 1555 1555 1.33 LINK C VAL A 653 N MLY A 654 1555 1555 1.33 LINK C MLY A 654 N VAL A 655 1555 1555 1.34 LINK C GLY A 657 N MLY A 658 1555 1555 1.34 LINK C MLY A 658 N LYS A 659 1555 1555 1.32 LINK C LEU A 662 N MLY A 663 1555 1555 1.33 LINK C MLY A 663 N TYR A 664 1555 1555 1.32 LINK MG MG A 703 O HOH A 862 1555 1555 2.17 LINK MG MG A 703 O HOH A 885 1555 1555 2.02 LINK MG MG A 703 O HOH A 891 1555 1555 2.13 LINK CH1 MLY A 658 O1 GOL A 701 1555 2656 1.38 CISPEP 1 ARG A 66 THR A 67 0 -9.75 SITE 1 AC1 6 ASP A 416 MLY A 658 HOH A 838 HOH A 842 SITE 2 AC1 6 HOH A 910 HOH A1059 SITE 1 AC2 9 GLU A 41 ASP A 387 MET A 415 HOH A 808 SITE 2 AC2 9 HOH A 841 HOH A 897 HOH A 904 HOH A1044 SITE 3 AC2 9 HOH A1140 SITE 1 AC3 6 GLN A 433 ASP A 451 HIS A 476 HOH A 862 SITE 2 AC3 6 HOH A 885 HOH A 891 CRYST1 186.690 45.741 80.514 90.00 94.05 90.00 C 1 2 1 4 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 0.005356 0.000000 0.000379 0.00000 SCALE2 0.000000 0.021862 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012451 0.00000