HEADER IMMUNE SYSTEM 01-SEP-23 8QF0 TITLE ATOMIC STRUCTURE OF WORMGDH COMPND MOL_ID: 1; COMPND 2 MOLECULE: GLUTAMATE DEHYDROGENASE; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HELIGMOSOMOIDES BAKERI; SOURCE 3 ORGANISM_TAXID: 375939; SOURCE 4 GENE: HPBE_LOCUS9300; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS XRAY, GDH, IMMUNE SYSTEM, EPIGENETIC EXPDTA X-RAY DIFFRACTION AUTHOR A.MOURAO,A.GEERLOF,M.SATTLER REVDAT 1 11-SEP-24 8QF0 0 JRNL AUTH A.MOURAO JRNL TITL ATOMIC STRUCTURE OF WORMGDH JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.86 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20.1_4487 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.86 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 144.93 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 100.05 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 155375 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.179 REMARK 3 R VALUE (WORKING SET) : 0.176 REMARK 3 FREE R VALUE : 0.200 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.990 REMARK 3 FREE R VALUE TEST SET COUNT : 7752 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1144.9300 - 5.0500 0.94 7752 454 0.1674 0.1929 REMARK 3 2 5.0500 - 4.0100 0.95 7558 384 0.1342 0.1603 REMARK 3 3 4.0100 - 3.5000 0.95 7534 358 0.1471 0.1647 REMARK 3 4 3.5000 - 3.1800 0.95 7502 366 0.1606 0.1853 REMARK 3 5 3.1800 - 2.9500 0.96 7492 347 0.1756 0.2144 REMARK 3 6 2.9500 - 2.7800 0.95 7468 356 0.1746 0.2072 REMARK 3 7 2.7800 - 2.6400 0.95 7424 395 0.1800 0.1900 REMARK 3 8 2.6400 - 2.5200 0.96 7474 336 0.1875 0.2203 REMARK 3 9 2.5200 - 2.4300 0.95 7376 392 0.1871 0.2180 REMARK 3 10 2.4300 - 2.3400 0.95 7402 384 0.1858 0.2069 REMARK 3 11 2.3400 - 2.2700 0.95 7392 380 0.1910 0.2041 REMARK 3 12 2.2700 - 2.2100 0.95 7383 411 0.1976 0.2229 REMARK 3 13 2.2100 - 2.1500 0.94 7314 445 0.2011 0.2199 REMARK 3 14 2.1500 - 2.0900 0.95 7382 403 0.2056 0.2288 REMARK 3 15 2.0900 - 2.0500 0.95 7345 382 0.2147 0.2342 REMARK 3 16 2.0500 - 2.0000 0.95 7391 393 0.2147 0.2260 REMARK 3 17 2.0000 - 1.9600 0.95 7321 392 0.2326 0.2548 REMARK 3 18 1.9600 - 1.9300 0.95 7451 368 0.2407 0.2749 REMARK 3 19 1.9300 - 1.8900 0.95 7277 381 0.2536 0.2597 REMARK 3 20 1.8900 - 1.8600 0.82 6418 392 0.2610 0.2666 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 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) : NULL REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.875 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.58 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 : 0.009 8039 REMARK 3 ANGLE : 1.051 10869 REMARK 3 CHIRALITY : 0.056 1183 REMARK 3 PLANARITY : 0.010 1411 REMARK 3 DIHEDRAL : 6.285 1103 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 8QF0 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 01-SEP-23. REMARK 100 THE DEPOSITION ID IS D_1292133084. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-NOV-21 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS-II REMARK 200 BEAMLINE : 17-ID-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : PSI PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 158711 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.860 REMARK 200 RESOLUTION RANGE LOW (A) : 144.930 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 20.00 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 2.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.86 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.07 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: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 70.44 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.16 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 12% V/V 2-PROPANOL, 50MM MES PH 6.0, REMARK 280 200MM POTASSIUM CHLORIDE, 6MM COBALT (III) HEXAMINE CHLORIDE, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 3 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z REMARK 290 6555 -X,-X+Y,-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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 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 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA 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 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 630 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 910 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 985 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 882 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 914 LIES ON A SPECIAL POSITION. REMARK 375 HOH B1016 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 GLN B 28 REMARK 465 VAL B 29 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 GLN A 28 CG CD OE1 NE2 REMARK 470 LYS A 46 CG CD CE NZ REMARK 470 GLU A 139 CG CD OE1 OE2 REMARK 470 GLU A 267 CG CD OE1 OE2 REMARK 470 ARG B 102 CG CD NE CZ NH1 NH2 REMARK 470 THR B 537 OG1 CG2 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 B 604 O HOH B 605 1.54 REMARK 500 O HOH A 607 O HOH A 938 1.72 REMARK 500 O HOH A 618 O HOH A 888 1.73 REMARK 500 O HOH A 622 O HOH A 970 1.75 REMARK 500 O HOH B 603 O HOH B 671 1.77 REMARK 500 O LEU A 456 O HOH A 601 1.78 REMARK 500 O ILE A 186 O HOH A 602 1.79 REMARK 500 O VAL B 111 O HOH B 601 1.81 REMARK 500 O ASP B 204 O HOH B 602 1.88 REMARK 500 O GLY A 488 O HOH A 603 1.93 REMARK 500 O SER A 71 O HOH A 604 1.94 REMARK 500 O MET A 72 O HOH A 605 1.97 REMARK 500 O HOH B 605 O HOH B 689 1.98 REMARK 500 O ASN A 520 O HOH A 606 1.98 REMARK 500 O HOH A 608 O HOH A 871 1.99 REMARK 500 N PHE B 99 O HOH B 601 1.99 REMARK 500 OH TYR B 149 O HOH B 603 2.01 REMARK 500 O HOH A 659 O HOH B 604 2.01 REMARK 500 O ALA B 87 O HOH B 604 2.01 REMARK 500 N GLY A 197 O HOH A 607 2.02 REMARK 500 O HOH A 608 O HOH A 836 2.03 REMARK 500 O ILE A 244 O HOH A 608 2.05 REMARK 500 OE1 GLN A 453 O HOH A 609 2.05 REMARK 500 OD1 ASN B 92 O HOH B 605 2.06 REMARK 500 O ASN A 373 O HOH A 610 2.08 REMARK 500 O HOH A 788 O HOH A 1069 2.10 REMARK 500 O GLU A 260 O HOH A 611 2.11 REMARK 500 OD2 ASP B 443 O HOH B 606 2.13 REMARK 500 O HOH B 730 O HOH B 960 2.15 REMARK 500 O HOH A 916 O HOH A 1079 2.15 REMARK 500 O HOH A 778 O HOH A 947 2.16 REMARK 500 O HOH A 795 O HOH A 885 2.17 REMARK 500 O HOH A 795 O HOH A 939 2.17 REMARK 500 O HOH A 718 O HOH B 633 2.18 REMARK 500 OG1 THR A 492 O HOH A 603 2.18 REMARK 500 O LYS B 46 O HOH B 607 2.18 REMARK 500 O HOH A 651 O HOH A 1028 2.18 REMARK 500 O HOH A 970 O HOH A 1048 2.18 REMARK 500 NH2 ARG A 247 O HOH A 612 2.18 REMARK 500 O PRO B 90 O HOH B 604 2.18 REMARK 500 O THR B 207 O HOH B 602 2.19 REMARK 500 O PHE B 99 O HOH B 601 2.19 REMARK 500 O HOH B 659 O HOH B 973 2.19 REMARK 500 O HOH A 860 O HOH A 978 2.19 REMARK 500 O HOH A 734 O HOH A 1023 2.19 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 604 O HOH B 661 4566 1.92 REMARK 500 O HOH A 762 O HOH A 891 2565 2.01 REMARK 500 O HOH A 603 O HOH A 739 2565 2.06 REMARK 500 O HOH A 605 O HOH B 750 4566 2.09 REMARK 500 O HOH A 605 O HOH B 956 4566 2.10 REMARK 500 O HOH A 967 O HOH A 1046 2565 2.18 REMARK 500 O HOH B 707 O HOH B 740 3455 2.19 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 PRO A 348 CA - N - CD ANGL. DEV. = -9.6 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 ASP A 32 23.96 -71.91 REMARK 500 SER A 69 114.89 -172.70 REMARK 500 ASP A 199 118.85 -164.94 REMARK 500 THR A 222 -99.72 -124.05 REMARK 500 ALA A 302 -13.03 72.94 REMARK 500 ASN A 318 106.77 -161.18 REMARK 500 PRO A 348 70.62 41.78 REMARK 500 ALA A 364 -118.75 -125.68 REMARK 500 ALA A 464 84.06 -152.02 REMARK 500 ASP B 32 21.00 -77.67 REMARK 500 PRO B 35 159.70 -46.12 REMARK 500 ASN B 41 63.27 -119.62 REMARK 500 ASP B 199 115.24 -166.57 REMARK 500 PRO B 201 -166.50 -78.16 REMARK 500 THR B 222 -96.06 -117.56 REMARK 500 ASN B 318 108.50 -161.88 REMARK 500 PRO B 348 71.15 39.93 REMARK 500 ALA B 364 -122.42 -130.85 REMARK 500 HIS B 370 -167.99 -124.47 REMARK 500 TYR B 411 -60.38 -98.88 REMARK 500 ALA B 464 87.30 -153.16 REMARK 500 PHE B 534 -116.29 -36.33 REMARK 500 THR B 535 -56.29 63.62 REMARK 500 PHE B 536 92.07 -53.16 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 GLU A 347 PRO A 348 -125.20 REMARK 500 GLU B 347 PRO B 348 -126.90 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 A1088 DISTANCE = 5.85 ANGSTROMS REMARK 525 HOH A1089 DISTANCE = 6.08 ANGSTROMS REMARK 525 HOH B1015 DISTANCE = 5.98 ANGSTROMS REMARK 525 HOH B1016 DISTANCE = 6.57 ANGSTROMS DBREF1 8QF0 A 28 537 UNP A0A183FP08_HELPZ DBREF2 8QF0 A A0A183FP08 28 537 DBREF1 8QF0 B 28 537 UNP A0A183FP08_HELPZ DBREF2 8QF0 B A0A183FP08 28 537 SEQRES 1 A 510 GLN VAL ILE ASP ASP LEU LYS PRO MET GLU GLU GLN SER SEQRES 2 A 510 ASN PRO SER PHE PHE LYS MET VAL ASP TYR TYR PHE ASP SEQRES 3 A 510 LYS GLY ALA THR VAL ILE GLU PRO LYS LEU VAL GLU GLU SEQRES 4 A 510 MET LYS SER ASN SER MET SER VAL MET ASP LYS LYS ASN SEQRES 5 A 510 LEU VAL SER GLY ILE LEU LYS ALA ILE LYS PRO VAL ASN SEQRES 6 A 510 LYS VAL LEU TYR ILE THR PHE PRO ILE ARG ARG ASP ASN SEQRES 7 A 510 GLY GLU PHE GLU VAL VAL GLU ALA TRP ARG ALA GLN HIS SEQRES 8 A 510 SER GLU HIS ARG THR PRO THR LYS GLY GLY ILE ARG TYR SEQRES 9 A 510 SER LEU ASP VAL CYS GLU ASP GLU VAL LYS ALA LEU SER SEQRES 10 A 510 ALA LEU MET THR TYR LYS CYS ALA ALA VAL ASP VAL PRO SEQRES 11 A 510 PHE GLY GLY ALA LYS GLY GLY VAL LYS ILE ASP PRO LYS SEQRES 12 A 510 MET TYR THR ASP TYR GLU ILE GLU LYS ILE THR ARG ARG SEQRES 13 A 510 ILE ALA ILE GLU PHE ALA LYS LYS GLY PHE LEU GLY PRO SEQRES 14 A 510 GLY VAL ASP VAL PRO ALA PRO ASP MET GLY THR GLY GLU SEQRES 15 A 510 ARG GLU MET GLY TRP ILE ALA ASP THR TYR ALA GLN THR SEQRES 16 A 510 ILE GLY HIS LEU ASP ARG ASP ALA SER ALA CYS ILE THR SEQRES 17 A 510 GLY LYS PRO ILE VAL ALA GLY GLY ILE HIS GLY ARG VAL SEQRES 18 A 510 SER ALA THR GLY ARG GLY VAL TRP LYS GLY LEU GLU VAL SEQRES 19 A 510 PHE ALA LYS GLU PRO GLU TYR MET GLU LYS ILE GLY LEU SEQRES 20 A 510 THR PRO GLY LEU PRO GLY LYS THR VAL ILE ILE GLN GLY SEQRES 21 A 510 PHE GLY ASN VAL GLY LEU HIS THR MET ARG TYR LEU HIS SEQRES 22 A 510 ARG ALA GLY SER LYS VAL VAL GLY ILE GLN GLU TRP ASP SEQRES 23 A 510 CYS ALA ILE HIS ASN PRO ALA GLY ILE HIS PRO LYS GLU SEQRES 24 A 510 LEU GLU ASP TRP ARG ASP GLN THR GLY SER ILE LYS ASN SEQRES 25 A 510 PHE PRO GLY ALA LYS ASN PHE GLU PRO PHE GLY ASP LEU SEQRES 26 A 510 ILE TYR GLU ALA CYS ASP ILE LEU VAL PRO ALA ALA CYS SEQRES 27 A 510 GLU LYS ALA ILE HIS LYS GLU ASN ALA GLY ARG ILE GLN SEQRES 28 A 510 ALA LYS ILE ILE ALA GLU ALA ALA ASN GLY PRO THR THR SEQRES 29 A 510 PRO ALA ALA ASP LYS ILE LEU LEU GLU ARG GLY ASN CYS SEQRES 30 A 510 LEU ILE ILE PRO ASP MET TYR VAL ASN SER GLY GLY VAL SEQRES 31 A 510 THR VAL SER TYR PHE GLU TRP LEU LYS ASN LEU ASN HIS SEQRES 32 A 510 VAL SER TYR GLY ARG LEU SER PHE LYS TYR GLU GLU ASP SEQRES 33 A 510 ALA ASN LEU MET LEU LEU GLN SER VAL GLN ASP SER LEU SEQRES 34 A 510 GLU LYS ALA ILE GLY LYS GLU ALA PRO VAL ARG PRO ASN SEQRES 35 A 510 ALA GLN PHE ALA ALA LYS ILE ALA GLY ALA SER GLU LYS SEQRES 36 A 510 ASP ILE VAL HIS SER GLY LEU GLU TYR THR MET ALA ARG SEQRES 37 A 510 SER GLY GLU ALA ILE ILE ARG THR ALA ARG LYS TYR ASN SEQRES 38 A 510 LEU GLY LEU ASP MET ARG THR ALA ALA TYR ALA ASN SER SEQRES 39 A 510 ILE GLU LYS VAL TYR ASN THR TYR ARG THR ALA GLY PHE SEQRES 40 A 510 THR PHE THR SEQRES 1 B 510 GLN VAL ILE ASP ASP LEU LYS PRO MET GLU GLU GLN SER SEQRES 2 B 510 ASN PRO SER PHE PHE LYS MET VAL ASP TYR TYR PHE ASP SEQRES 3 B 510 LYS GLY ALA THR VAL ILE GLU PRO LYS LEU VAL GLU GLU SEQRES 4 B 510 MET LYS SER ASN SER MET SER VAL MET ASP LYS LYS ASN SEQRES 5 B 510 LEU VAL SER GLY ILE LEU LYS ALA ILE LYS PRO VAL ASN SEQRES 6 B 510 LYS VAL LEU TYR ILE THR PHE PRO ILE ARG ARG ASP ASN SEQRES 7 B 510 GLY GLU PHE GLU VAL VAL GLU ALA TRP ARG ALA GLN HIS SEQRES 8 B 510 SER GLU HIS ARG THR PRO THR LYS GLY GLY ILE ARG TYR SEQRES 9 B 510 SER LEU ASP VAL CYS GLU ASP GLU VAL LYS ALA LEU SER SEQRES 10 B 510 ALA LEU MET THR TYR LYS CYS ALA ALA VAL ASP VAL PRO SEQRES 11 B 510 PHE GLY GLY ALA LYS GLY GLY VAL LYS ILE ASP PRO LYS SEQRES 12 B 510 MET TYR THR ASP TYR GLU ILE GLU LYS ILE THR ARG ARG SEQRES 13 B 510 ILE ALA ILE GLU PHE ALA LYS LYS GLY PHE LEU GLY PRO SEQRES 14 B 510 GLY VAL ASP VAL PRO ALA PRO ASP MET GLY THR GLY GLU SEQRES 15 B 510 ARG GLU MET GLY TRP ILE ALA ASP THR TYR ALA GLN THR SEQRES 16 B 510 ILE GLY HIS LEU ASP ARG ASP ALA SER ALA CYS ILE THR SEQRES 17 B 510 GLY LYS PRO ILE VAL ALA GLY GLY ILE HIS GLY ARG VAL SEQRES 18 B 510 SER ALA THR GLY ARG GLY VAL TRP LYS GLY LEU GLU VAL SEQRES 19 B 510 PHE ALA LYS GLU PRO GLU TYR MET GLU LYS ILE GLY LEU SEQRES 20 B 510 THR PRO GLY LEU PRO GLY LYS THR VAL ILE ILE GLN GLY SEQRES 21 B 510 PHE GLY ASN VAL GLY LEU HIS THR MET ARG TYR LEU HIS SEQRES 22 B 510 ARG ALA GLY SER LYS VAL VAL GLY ILE GLN GLU TRP ASP SEQRES 23 B 510 CYS ALA ILE HIS ASN PRO ALA GLY ILE HIS PRO LYS GLU SEQRES 24 B 510 LEU GLU ASP TRP ARG ASP GLN THR GLY SER ILE LYS ASN SEQRES 25 B 510 PHE PRO GLY ALA LYS ASN PHE GLU PRO PHE GLY ASP LEU SEQRES 26 B 510 ILE TYR GLU ALA CYS ASP ILE LEU VAL PRO ALA ALA CYS SEQRES 27 B 510 GLU LYS ALA ILE HIS LYS GLU ASN ALA GLY ARG ILE GLN SEQRES 28 B 510 ALA LYS ILE ILE ALA GLU ALA ALA ASN GLY PRO THR THR SEQRES 29 B 510 PRO ALA ALA ASP LYS ILE LEU LEU GLU ARG GLY ASN CYS SEQRES 30 B 510 LEU ILE ILE PRO ASP MET TYR VAL ASN SER GLY GLY VAL SEQRES 31 B 510 THR VAL SER TYR PHE GLU TRP LEU LYS ASN LEU ASN HIS SEQRES 32 B 510 VAL SER TYR GLY ARG LEU SER PHE LYS TYR GLU GLU ASP SEQRES 33 B 510 ALA ASN LEU MET LEU LEU GLN SER VAL GLN ASP SER LEU SEQRES 34 B 510 GLU LYS ALA ILE GLY LYS GLU ALA PRO VAL ARG PRO ASN SEQRES 35 B 510 ALA GLN PHE ALA ALA LYS ILE ALA GLY ALA SER GLU LYS SEQRES 36 B 510 ASP ILE VAL HIS SER GLY LEU GLU TYR THR MET ALA ARG SEQRES 37 B 510 SER GLY GLU ALA ILE ILE ARG THR ALA ARG LYS TYR ASN SEQRES 38 B 510 LEU GLY LEU ASP MET ARG THR ALA ALA TYR ALA ASN SER SEQRES 39 B 510 ILE GLU LYS VAL TYR ASN THR TYR ARG THR ALA GLY PHE SEQRES 40 B 510 THR PHE THR FORMUL 3 HOH *905(H2 O) HELIX 1 AA1 GLN A 28 LYS A 34 5 7 HELIX 2 AA2 PRO A 35 GLN A 39 5 5 HELIX 3 AA3 SER A 43 MET A 67 1 25 HELIX 4 AA4 SER A 73 LYS A 89 1 17 HELIX 5 AA5 CYS A 136 VAL A 154 1 19 HELIX 6 AA6 ASP A 168 TYR A 172 5 5 HELIX 7 AA7 THR A 173 LYS A 191 1 19 HELIX 8 AA8 GLY A 208 THR A 222 1 15 HELIX 9 AA9 ASP A 229 ILE A 234 5 6 HELIX 10 AB1 PRO A 238 GLY A 242 5 5 HELIX 11 AB2 SER A 249 LYS A 264 1 16 HELIX 12 AB3 GLU A 265 ILE A 272 1 8 HELIX 13 AB4 GLY A 289 ARG A 301 1 13 HELIX 14 AB5 ALA A 302 SER A 304 5 3 HELIX 15 AB6 HIS A 323 GLY A 335 1 13 HELIX 16 AB7 PRO A 348 GLU A 355 5 8 HELIX 17 AB8 ASN A 373 ILE A 377 5 5 HELIX 18 AB9 THR A 391 GLY A 402 1 12 HELIX 19 AC1 PRO A 408 ASN A 413 1 6 HELIX 20 AC2 SER A 414 HIS A 430 1 17 HELIX 21 AC3 SER A 437 GLY A 461 1 25 HELIX 22 AC4 ASN A 469 GLY A 478 1 10 HELIX 23 AC5 SER A 480 TYR A 507 1 28 HELIX 24 AC6 ASP A 512 GLY A 533 1 22 HELIX 25 AC7 ILE B 30 LYS B 34 5 5 HELIX 26 AC8 PRO B 35 GLN B 39 5 5 HELIX 27 AC9 SER B 43 MET B 67 1 25 HELIX 28 AD1 SER B 73 LYS B 89 1 17 HELIX 29 AD2 CYS B 136 VAL B 154 1 19 HELIX 30 AD3 ASP B 168 TYR B 172 5 5 HELIX 31 AD4 THR B 173 LYS B 191 1 19 HELIX 32 AD5 GLY B 208 THR B 222 1 15 HELIX 33 AD6 ASP B 229 ILE B 234 5 6 HELIX 34 AD7 PRO B 238 GLY B 242 5 5 HELIX 35 AD8 SER B 249 LYS B 264 1 16 HELIX 36 AD9 GLU B 265 ILE B 272 1 8 HELIX 37 AE1 GLY B 289 ARG B 301 1 13 HELIX 38 AE2 HIS B 323 GLY B 335 1 13 HELIX 39 AE3 PRO B 348 GLU B 355 5 8 HELIX 40 AE4 ASN B 373 ILE B 377 5 5 HELIX 41 AE5 THR B 391 GLY B 402 1 12 HELIX 42 AE6 PRO B 408 ASN B 413 1 6 HELIX 43 AE7 SER B 414 HIS B 430 1 17 HELIX 44 AE8 SER B 437 GLY B 461 1 25 HELIX 45 AE9 ASN B 469 ALA B 479 1 11 HELIX 46 AF1 SER B 480 TYR B 507 1 28 HELIX 47 AF2 ASP B 512 GLY B 533 1 22 SHEET 1 AA1 8 ILE A 129 TYR A 131 0 SHEET 2 AA1 8 GLY A 159 VAL A 165 1 O VAL A 165 N ARG A 130 SHEET 3 AA1 8 PHE A 108 GLN A 117 -1 N ALA A 116 O LYS A 162 SHEET 4 AA1 8 LYS A 93 ARG A 102 -1 N PHE A 99 O VAL A 111 SHEET 5 AA1 8 LYS B 93 ARG B 102 -1 O TYR B 96 N VAL A 94 SHEET 6 AA1 8 PHE B 108 GLN B 117 -1 O GLN B 117 N LYS B 93 SHEET 7 AA1 8 GLY B 159 VAL B 165 -1 O LYS B 162 N ALA B 116 SHEET 8 AA1 8 ILE B 129 TYR B 131 1 N ARG B 130 O VAL B 165 SHEET 1 AA210 ASP A 199 VAL A 200 0 SHEET 2 AA210 THR A 125 LYS A 126 1 N THR A 125 O VAL A 200 SHEET 3 AA210 GLY A 159 VAL A 165 1 O ALA A 161 N LYS A 126 SHEET 4 AA210 PHE A 108 GLN A 117 -1 N ALA A 116 O LYS A 162 SHEET 5 AA210 LYS A 93 ARG A 102 -1 N PHE A 99 O VAL A 111 SHEET 6 AA210 LYS B 93 ARG B 102 -1 O TYR B 96 N VAL A 94 SHEET 7 AA210 PHE B 108 GLN B 117 -1 O GLN B 117 N LYS B 93 SHEET 8 AA210 GLY B 159 VAL B 165 -1 O LYS B 162 N ALA B 116 SHEET 9 AA210 THR B 125 LYS B 126 1 N LYS B 126 O ALA B 161 SHEET 10 AA210 ASP B 199 VAL B 200 1 O VAL B 200 N THR B 125 SHEET 1 AA3 7 LYS A 344 ASN A 345 0 SHEET 2 AA3 7 ALA A 315 HIS A 317 -1 N HIS A 317 O LYS A 344 SHEET 3 AA3 7 LYS A 305 GLN A 310 -1 N ILE A 309 O ILE A 316 SHEET 4 AA3 7 THR A 282 GLN A 286 1 N VAL A 283 O LYS A 305 SHEET 5 AA3 7 ILE A 359 PRO A 362 1 O VAL A 361 N ILE A 284 SHEET 6 AA3 7 ILE A 381 ALA A 383 1 O ILE A 381 N LEU A 360 SHEET 7 AA3 7 LEU A 405 ILE A 407 1 O ILE A 407 N ILE A 382 SHEET 1 AA4 7 LYS B 344 ASN B 345 0 SHEET 2 AA4 7 ALA B 315 HIS B 317 -1 N HIS B 317 O LYS B 344 SHEET 3 AA4 7 LYS B 305 GLN B 310 -1 N ILE B 309 O ILE B 316 SHEET 4 AA4 7 THR B 282 GLN B 286 1 N VAL B 283 O LYS B 305 SHEET 5 AA4 7 ILE B 359 PRO B 362 1 O VAL B 361 N ILE B 284 SHEET 6 AA4 7 ILE B 381 ALA B 383 1 O ILE B 381 N LEU B 360 SHEET 7 AA4 7 LEU B 405 ILE B 407 1 O ILE B 407 N ILE B 382 CISPEP 1 THR A 123 PRO A 124 0 4.70 CISPEP 2 THR B 123 PRO B 124 0 3.59 CRYST1 149.456 149.456 144.928 90.00 90.00 120.00 P 3 2 1 12 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 0.006691 0.003863 0.000000 0.00000 SCALE2 0.000000 0.007726 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006900 0.00000 MASTER 419 0 0 47 32 0 0 6 8765 2 0 80 END