HEADER LYASE 03-APR-21 7MD9 TITLE CRYSTAL STRUCTURE OF STAPHYLOCOCCUS AUREUS CYSTATHIONINE GAMMA LYASE TITLE 2 HOLOENZYME Y103A MUTANT COMPND MOL_ID: 1; COMPND 2 MOLECULE: BIFUNCTIONAL CYSTATHIONINE GAMMA-LYASE/HOMOCYSTEINE COMPND 3 DESULFHYDRASE; COMPND 4 CHAIN: H; COMPND 5 SYNONYM: CYSTATHIONINE BETA-LYASE,CYSTATHIONINE GAMMA-LYASE, COMPND 6 CYSTATHIONINE GAMMA-SYNTHASE; COMPND 7 EC: 4.4.1.1,4.4.1.8,2.5.1.48; COMPND 8 ENGINEERED: YES; COMPND 9 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STAPHYLOCOCCUS AUREUS; SOURCE 3 ORGANISM_TAXID: 1280; SOURCE 4 GENE: MCCB; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS AMINO-ACID BIOSYNTHESIS, CYSTEINE BIOSYNTHESIS, HYDROGEN SULFIDE KEYWDS 2 PRODUCTION, PLP DEPENDENT ENZYME, LYASE EXPDTA X-RAY DIFFRACTION AUTHOR A.NUTHANAKANTI,A.SERGANOV,A.KAUSHIK REVDAT 3 15-NOV-23 7MD9 1 REMARK REVDAT 2 18-OCT-23 7MD9 1 REMARK REVDAT 1 23-JUN-21 7MD9 0 JRNL AUTH K.SHATALIN,A.NUTHANAKANTI,A.KAUSHIK,D.SHISHOV,A.PESELIS, JRNL AUTH 2 I.SHAMOVSKY,B.PANI,M.LECHPAMMER,N.VASILYEV,E.SHATALINA, JRNL AUTH 3 D.REBATCHOUK,A.MIRONOV,P.FEDICHEV,A.SERGANOV,E.NUDLER JRNL TITL INHIBITORS OF BACTERIAL H 2 S BIOGENESIS TARGETING JRNL TITL 2 ANTIBIOTIC RESISTANCE AND TOLERANCE. JRNL REF SCIENCE V. 372 1169 2021 JRNL REFN ESSN 1095-9203 JRNL PMID 34112687 JRNL DOI 10.1126/SCIENCE.ABD8377 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.14_3260 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 : CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.86 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 3 NUMBER OF REFLECTIONS : 73637 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.185 REMARK 3 R VALUE (WORKING SET) : 0.185 REMARK 3 FREE R VALUE : 0.205 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 2.720 REMARK 3 FREE R VALUE TEST SET COUNT : 3805 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 29.8600 - 5.3900 0.99 5048 146 0.1587 0.2008 REMARK 3 2 5.3900 - 4.2800 0.91 4625 134 0.1363 0.1633 REMARK 3 3 4.2800 - 3.7400 0.93 4752 123 0.1345 0.1230 REMARK 3 4 3.7400 - 3.4000 0.97 4973 142 0.1580 0.1488 REMARK 3 5 3.4000 - 3.1600 0.99 5027 140 0.1688 0.2016 REMARK 3 6 3.1600 - 2.9700 1.00 5101 139 0.1867 0.2247 REMARK 3 7 2.9700 - 2.8200 1.00 5084 142 0.1955 0.2082 REMARK 3 8 2.8200 - 2.7000 1.00 5053 145 0.1964 0.2267 REMARK 3 9 2.7000 - 2.6000 1.00 5101 142 0.1997 0.2569 REMARK 3 10 2.6000 - 2.5100 1.00 5114 148 0.2072 0.2274 REMARK 3 11 2.5100 - 2.4300 1.00 5057 141 0.2076 0.2630 REMARK 3 12 2.4300 - 2.3600 1.00 5110 142 0.2121 0.2232 REMARK 3 13 2.3600 - 2.3000 1.00 5069 143 0.2000 0.2204 REMARK 3 14 2.3000 - 2.2400 1.00 5069 139 0.1949 0.2153 REMARK 3 15 2.2400 - 2.1900 1.00 5066 143 0.1910 0.2025 REMARK 3 16 2.1900 - 2.1400 1.00 5121 145 0.1993 0.1986 REMARK 3 17 2.1400 - 2.1000 1.00 5059 143 0.2059 0.2300 REMARK 3 18 2.1000 - 2.0600 1.00 5093 140 0.2119 0.2218 REMARK 3 19 2.0600 - 2.0200 1.00 5093 140 0.2185 0.2592 REMARK 3 20 2.0200 - 1.9900 1.00 5080 142 0.2279 0.2680 REMARK 3 21 1.9900 - 1.9600 1.00 5060 143 0.2239 0.2090 REMARK 3 22 1.9600 - 1.9300 1.00 5100 140 0.2380 0.2662 REMARK 3 23 1.9300 - 1.9000 0.99 5051 140 0.2560 0.2299 REMARK 3 24 1.9000 - 1.8700 0.99 5042 143 0.2637 0.2702 REMARK 3 25 1.8700 - 1.8500 1.00 5145 143 0.2743 0.3169 REMARK 3 26 1.8500 - 1.8200 1.00 5076 146 0.2930 0.3295 REMARK 3 27 1.8200 - 1.8000 0.95 4817 131 0.3065 0.3604 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) : 0.176 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.658 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 23.89 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 30.04 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 : 0.007 2978 REMARK 3 ANGLE : 0.868 4058 REMARK 3 CHIRALITY : 0.056 489 REMARK 3 PLANARITY : 0.006 520 REMARK 3 DIHEDRAL : 3.788 2423 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 7MD9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 05-APR-21. REMARK 100 THE DEPOSITION ID IS D_1000256006. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 31-JAN-20 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 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-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.91956 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 73637 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 7.700 REMARK 200 R MERGE (I) : 0.09200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 219.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.84 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.4 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 1.04500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 12.40 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: PDB ENTRY 4IXZ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 74.18 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.76 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M HEPES SODIUM, PH 7.5, 1.3 M TRI REMARK 280 -SODIUM CITRATE, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 41 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 3555 -Y,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X,Z+3/4 REMARK 290 5555 -X+1/2,Y,-Z+3/4 REMARK 290 6555 X,-Y+1/2,-Z+1/4 REMARK 290 7555 Y+1/2,X+1/2,-Z+1/2 REMARK 290 8555 -Y,-X,-Z REMARK 290 9555 X+1/2,Y+1/2,Z+1/2 REMARK 290 10555 -X,-Y,Z REMARK 290 11555 -Y+1/2,X,Z+3/4 REMARK 290 12555 Y,-X+1/2,Z+1/4 REMARK 290 13555 -X,Y+1/2,-Z+1/4 REMARK 290 14555 X+1/2,-Y,-Z+3/4 REMARK 290 15555 Y,X,-Z REMARK 290 16555 -Y+1/2,-X+1/2,-Z+1/2 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 52.44600 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 52.44600 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 143.44950 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 52.44600 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 71.72475 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 52.44600 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 215.17425 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 52.44600 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 215.17425 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 52.44600 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 71.72475 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 52.44600 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 52.44600 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 143.44950 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 1.000000 0.000000 0.000000 52.44600 REMARK 290 SMTRY2 9 0.000000 1.000000 0.000000 52.44600 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 143.44950 REMARK 290 SMTRY1 10 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 10 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 11 0.000000 -1.000000 0.000000 52.44600 REMARK 290 SMTRY2 11 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 1.000000 215.17425 REMARK 290 SMTRY1 12 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 12 -1.000000 0.000000 0.000000 52.44600 REMARK 290 SMTRY3 12 0.000000 0.000000 1.000000 71.72475 REMARK 290 SMTRY1 13 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 52.44600 REMARK 290 SMTRY3 13 0.000000 0.000000 -1.000000 71.72475 REMARK 290 SMTRY1 14 1.000000 0.000000 0.000000 52.44600 REMARK 290 SMTRY2 14 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 14 0.000000 0.000000 -1.000000 215.17425 REMARK 290 SMTRY1 15 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 15 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 15 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 16 0.000000 -1.000000 0.000000 52.44600 REMARK 290 SMTRY2 16 -1.000000 0.000000 0.000000 52.44600 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 143.44950 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: 21520 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 45370 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -170.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: H 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 0.000000 -1.000000 0.000000 104.89200 REMARK 350 BIOMT2 2 -1.000000 0.000000 0.000000 104.89200 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 350 BIOMT1 3 -1.000000 0.000000 0.000000 104.89200 REMARK 350 BIOMT2 3 0.000000 -1.000000 0.000000 104.89200 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 4 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 4 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 4 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 H 509 LIES ON A SPECIAL POSITION. REMARK 375 HOH H 766 LIES ON A SPECIAL POSITION. REMARK 375 HOH H 847 LIES ON A SPECIAL POSITION. REMARK 375 HOH H 917 LIES ON A SPECIAL POSITION. 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 LYS H 88 CE NZ REMARK 470 LYS H 155 CE NZ REMARK 470 LYS H 162 CE NZ REMARK 470 LYS H 215 CE NZ REMARK 470 LYS H 303 CD CE NZ 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 NZ LYS H 349 O HOH H 501 1.85 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 H 667 O HOH H 805 10665 2.12 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 GLU H 44 -24.01 -142.94 REMARK 500 VAL H 109 -63.02 -109.60 REMARK 500 THR H 176 162.96 68.97 REMARK 500 LLP H 196 -116.61 -95.51 REMARK 500 GLN H 271 -109.45 -96.57 REMARK 500 SER H 323 -176.24 74.08 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 H 919 DISTANCE = 5.98 ANGSTROMS 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 NA H 402 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS H 9 O REMARK 620 2 GLY H 11 O 99.5 REMARK 620 3 HOH H 510 O 72.0 53.5 REMARK 620 4 HOH H 669 O 93.8 87.8 133.6 REMARK 620 5 HOH H 674 O 173.8 83.6 106.2 91.6 REMARK 620 6 HOH H 746 O 89.7 170.0 134.3 87.8 87.5 REMARK 620 7 HOH H 754 O 69.3 120.7 68.2 148.2 104.5 66.2 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA H 401 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH H 503 O REMARK 620 2 HOH H 540 O 90.4 REMARK 620 3 HOH H 865 O 78.9 86.9 REMARK 620 4 HOH H 891 O 168.0 85.3 89.7 REMARK 620 5 HOH H 892 O 112.0 99.8 166.9 79.7 REMARK 620 N 1 2 3 4 DBREF 7MD9 H 2 380 UNP X5E0F1 X5E0F1_STAAU 2 380 SEQADV 7MD9 SER H 1 UNP X5E0F1 EXPRESSION TAG SEQADV 7MD9 ALA H 103 UNP X5E0F1 TYR 103 ENGINEERED MUTATION SEQRES 1 H 380 SER ASN LYS LYS THR LYS LEU ILE HIS GLY GLY HIS THR SEQRES 2 H 380 THR ASP ASP TYR THR GLY ALA VAL THR THR PRO ILE TYR SEQRES 3 H 380 GLN THR SER THR TYR LEU GLN ASP ASP ILE GLY ASP LEU SEQRES 4 H 380 ARG GLN GLY TYR GLU TYR SER ARG THR ALA ASN PRO THR SEQRES 5 H 380 ARG SER SER VAL GLU SER VAL ILE ALA THR LEU GLU ASN SEQRES 6 H 380 GLY LYS HIS GLY PHE ALA PHE SER SER GLY VAL ALA ALA SEQRES 7 H 380 ILE SER ALA VAL VAL MET LEU LEU ASP LYS GLY ASP HIS SEQRES 8 H 380 ILE ILE LEU ASN SER ASP VAL TYR GLY GLY THR ALA ARG SEQRES 9 H 380 ALA LEU THR LYS VAL PHE THR ARG PHE GLY ILE GLU VAL SEQRES 10 H 380 ASP PHE VAL ASP THR THR HIS THR ASP SER ILE VAL GLN SEQRES 11 H 380 ALA ILE ARG PRO THR THR LYS MET LEU PHE ILE GLU THR SEQRES 12 H 380 PRO SER ASN PRO LEU LEU ARG VAL THR ASP ILE LYS LYS SEQRES 13 H 380 SER ALA GLU ILE ALA LYS GLU HIS GLY LEU ILE SER VAL SEQRES 14 H 380 VAL ASP ASN THR PHE MET THR PRO TYR TYR GLN ASN PRO SEQRES 15 H 380 LEU ASP LEU GLY ILE ASP ILE VAL LEU HIS SER ALA THR SEQRES 16 H 380 LLP TYR LEU GLY GLY HIS SER ASP VAL VAL ALA GLY LEU SEQRES 17 H 380 VAL ALA THR SER ASP ASP LYS LEU ALA GLU ARG LEU ALA SEQRES 18 H 380 PHE ILE SER ASN SER THR GLY GLY ILE LEU GLY PRO GLN SEQRES 19 H 380 ASP SER TYR LEU LEU VAL ARG GLY ILE LYS THR LEU GLY SEQRES 20 H 380 LEU ARG MET GLU GLN ILE ASN ARG SER VAL ILE GLU ILE SEQRES 21 H 380 ILE LYS MET LEU GLN ALA HIS PRO ALA VAL GLN GLN VAL SEQRES 22 H 380 PHE HIS PRO SER ILE GLU SER HIS LEU ASN HIS ASP VAL SEQRES 23 H 380 HIS MET ALA GLN ALA ASP GLY HIS THR GLY VAL ILE ALA SEQRES 24 H 380 PHE GLU VAL LYS ASN THR GLU SER ALA LYS GLN LEU ILE SEQRES 25 H 380 LYS ALA THR SER TYR TYR THR LEU ALA GLU SER LEU GLY SEQRES 26 H 380 ALA VAL GLU SER LEU ILE SER VAL PRO ALA LEU MET THR SEQRES 27 H 380 HIS ALA SER ILE PRO ALA ASP ILE ARG ALA LYS GLU GLY SEQRES 28 H 380 ILE THR ASP GLY LEU VAL ARG ILE SER VAL GLY ILE GLU SEQRES 29 H 380 ASP THR GLU ASP LEU VAL ASP ASP LEU LYS GLN ALA LEU SEQRES 30 H 380 ASP THR LEU MODRES 7MD9 LLP H 196 LYS MODIFIED RESIDUE HET LLP H 196 24 HET NA H 401 1 HET NA H 402 1 HETNAM LLP (2S)-2-AMINO-6-[[3-HYDROXY-2-METHYL-5- HETNAM 2 LLP (PHOSPHONOOXYMETHYL)PYRIDIN-4- HETNAM 3 LLP YL]METHYLIDENEAMINO]HEXANOIC ACID HETNAM NA SODIUM ION HETSYN LLP N'-PYRIDOXYL-LYSINE-5'-MONOPHOSPHATE FORMUL 1 LLP C14 H22 N3 O7 P FORMUL 2 NA 2(NA 1+) FORMUL 4 HOH *419(H2 O) HELIX 1 AA1 ASN H 2 GLY H 10 1 9 HELIX 2 AA2 ASN H 50 GLU H 64 1 15 HELIX 3 AA3 SER H 74 MET H 84 1 11 HELIX 4 AA4 TYR H 99 VAL H 109 1 11 HELIX 5 AA5 PHE H 110 GLY H 114 5 5 HELIX 6 AA6 THR H 125 ILE H 132 1 8 HELIX 7 AA7 ASP H 153 HIS H 164 1 12 HELIX 8 AA8 MET H 175 GLN H 180 1 6 HELIX 9 AA9 ASN H 181 GLY H 186 5 6 HELIX 10 AB1 ASP H 213 GLY H 228 1 16 HELIX 11 AB2 GLY H 232 THR H 245 1 14 HELIX 12 AB3 THR H 245 HIS H 267 1 23 HELIX 13 AB4 ASN H 283 ALA H 291 1 9 HELIX 14 AB5 ASN H 304 THR H 315 1 12 HELIX 15 AB6 VAL H 333 THR H 338 1 6 HELIX 16 AB7 PRO H 343 GLY H 351 1 9 HELIX 17 AB8 ASP H 365 THR H 379 1 15 SHEET 1 AA1 7 HIS H 68 PHE H 72 0 SHEET 2 AA1 7 GLY H 207 THR H 211 -1 O GLY H 207 N PHE H 72 SHEET 3 AA1 7 ILE H 189 SER H 193 -1 N VAL H 190 O ALA H 210 SHEET 4 AA1 7 ILE H 167 ASP H 171 1 N VAL H 170 O LEU H 191 SHEET 5 AA1 7 THR H 136 GLU H 142 1 N LYS H 137 O ILE H 167 SHEET 6 AA1 7 HIS H 91 ASN H 95 1 N ILE H 93 O PHE H 140 SHEET 7 AA1 7 GLU H 116 VAL H 120 1 O VAL H 120 N LEU H 94 SHEET 1 AA2 5 VAL H 273 PHE H 274 0 SHEET 2 AA2 5 VAL H 297 GLU H 301 -1 O ALA H 299 N PHE H 274 SHEET 3 AA2 5 LEU H 356 SER H 360 -1 O VAL H 357 N PHE H 300 SHEET 4 AA2 5 SER H 329 SER H 332 -1 N LEU H 330 O SER H 360 SHEET 5 AA2 5 TYR H 318 LEU H 320 1 N THR H 319 O SER H 329 LINK C THR H 195 N LLP H 196 1555 1555 1.33 LINK C LLP H 196 N TYR H 197 1555 1555 1.33 LINK O HIS H 9 NA NA H 402 1555 1555 2.41 LINK O GLY H 11 NA NA H 402 1555 1555 2.44 LINK NA NA H 401 O HOH H 503 1555 1555 2.81 LINK NA NA H 401 O HOH H 540 1555 1555 2.51 LINK NA NA H 401 O HOH H 865 1555 1555 2.64 LINK NA NA H 401 O HOH H 891 1555 1555 2.81 LINK NA NA H 401 O HOH H 892 1555 1555 2.45 LINK NA NA H 402 O HOH H 510 1555 1555 2.83 LINK NA NA H 402 O HOH H 669 1555 1555 2.54 LINK NA NA H 402 O HOH H 674 1555 1555 2.50 LINK NA NA H 402 O HOH H 746 1555 1555 3.10 LINK NA NA H 402 O HOH H 754 1555 1555 2.79 CISPEP 1 THR H 143 PRO H 144 0 -5.72 CISPEP 2 ASN H 146 PRO H 147 0 -3.22 CRYST1 104.892 104.892 286.899 90.00 90.00 90.00 I 41 2 2 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 0.009534 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009534 0.000000 0.00000 SCALE3 0.000000 0.000000 0.003486 0.00000