HEADER LIGASE 09-AUG-13 4C13 TITLE X-RAY CRYSTAL STRUCTURE OF STAPHYLOCOCCUS AUREUS MURE WITH UDP-MURNAC- TITLE 2 ALA-GLU-LYS COMPND MOL_ID: 1; COMPND 2 MOLECULE: UDP-N-ACETYLMURAMOYL-L-ALANYL-D-GLUTAMATE--L-LYSINE LIGASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: L-LYSINE-ADDING ENZYME, UDP-MURNAC-L-ALA-D-GLU\:L-LYS COMPND 5 LIGASE, UDP-MURNAC-TRIPEPTIDE SYNTHETASE, UDP-N-ACETYLMURAMYL- COMPND 6 TRIPEPTIDE SYNTHETASE; COMPND 7 EC: 6.3.2.7; COMPND 8 ENGINEERED: YES; COMPND 9 OTHER_DETAILS: K219 HAS BEEN MODIFIED BY CARBAMOYLATION SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STAPHYLOCOCCUS AUREUS; SOURCE 3 ORGANISM_TAXID: 1280; SOURCE 4 STRAIN: 8325; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VARIANT: PLYSS; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_VECTOR: PET; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PET2160 KEYWDS LIGASE, MURE EXPDTA X-RAY DIFFRACTION AUTHOR K.M.RUANE,D.I.ROPER,V.FULOP,H.BARRETEAU,A.BONIFACE,S.DEMENTIN, AUTHOR 2 D.BLANOT,D.MENGIN-LECREULX,S.GOBEC,A.DESSEN,C.G.DOWSON,A.J.LLOYD REVDAT 7 17-MAR-21 4C13 1 JRNL REMARK LINK REVDAT 6 20-JUN-18 4C13 1 REMARK REVDAT 5 13-SEP-17 4C13 1 REMARK REVDAT 4 28-JUN-17 4C13 1 REMARK REVDAT 3 27-NOV-13 4C13 1 JRNL REVDAT 2 09-OCT-13 4C13 1 JRNL REVDAT 1 02-OCT-13 4C13 0 JRNL AUTH L.WANG,X.SHAO,T.ZHONG,Y.WU,A.XU,X.SUN,H.GAO,Y.LIU,T.LAN, JRNL AUTH 2 Y.TONG,X.TAO,W.DU,W.WANG,Y.CHEN,T.LI,X.MENG,H.DENG,B.YANG, JRNL AUTH 3 Q.HE,M.YING,Y.RAO JRNL TITL DISCOVERY OF A FIRST-IN-CLASS CDK2 SELECTIVE DEGRADER FOR JRNL TITL 2 AML DIFFERENTIATION THERAPY. JRNL REF NAT.CHEM.BIOL. 2021 JRNL REFN ESSN 1552-4469 JRNL PMID 33664520 JRNL DOI 10.1038/S41589-021-00742-5 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH K.M.RUANE,A.J.LLOYD,V.FULOP,C.G.DOWSON,H.BARRETEAU, REMARK 1 AUTH 2 A.BONIFACE,S.DEMENTIN,D.BLANOT,D.MENGIN-LECREULX,S.GOBEC, REMARK 1 AUTH 3 A.DESSEN,D.I.ROPER REMARK 1 TITL SPECIFICITY DETERMINANTS FOR LYSINE INCORPORATION IN REMARK 1 TITL 2 STAPHYLOCOCCUS AUREUS PEPTIDOGLYCAN AS REVEALED BY THE REMARK 1 TITL 3 STRUCTURE OF A MURE ENZYME TERNARY COMPLEX. REMARK 1 REF J.BIOL.CHEM. V. 288 33439 2013 REMARK 1 REFN ISSN 0021-9258 REMARK 1 PMID 24064214 REMARK 1 DOI 10.1074/JBC.M113.508135 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.6.0117 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 78.86 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 94.4 REMARK 3 NUMBER OF REFLECTIONS : 42467 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.198 REMARK 3 R VALUE (WORKING SET) : 0.196 REMARK 3 FREE R VALUE : 0.241 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2271 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.95 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2984 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 92.18 REMARK 3 BIN R VALUE (WORKING SET) : 0.2940 REMARK 3 BIN FREE R VALUE SET COUNT : 138 REMARK 3 BIN FREE R VALUE : 0.3370 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3766 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 76 REMARK 3 SOLVENT ATOMS : 213 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.83 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.08000 REMARK 3 B22 (A**2) : 1.62000 REMARK 3 B33 (A**2) : -0.58000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.48000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.152 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.147 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.102 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 6.680 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.944 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.917 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3932 ; 0.015 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5340 ; 1.724 ; 1.986 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 493 ; 6.322 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 165 ;36.532 ;24.970 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 660 ;15.145 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 16 ;22.092 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 619 ; 0.108 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2929 ; 0.009 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 1 A 326 REMARK 3 ORIGIN FOR THE GROUP (A): -13.8597 -6.7507 -0.7370 REMARK 3 T TENSOR REMARK 3 T11: 0.0106 T22: 0.0136 REMARK 3 T33: 0.0506 T12: 0.0057 REMARK 3 T13: 0.0033 T23: -0.0070 REMARK 3 L TENSOR REMARK 3 L11: 0.3938 L22: 0.3901 REMARK 3 L33: 0.8060 L12: 0.0250 REMARK 3 L13: 0.1072 L23: -0.0506 REMARK 3 S TENSOR REMARK 3 S11: 0.0013 S12: -0.0303 S13: -0.0230 REMARK 3 S21: 0.0263 S22: 0.0058 S23: 0.0261 REMARK 3 S31: 0.0296 S32: -0.0421 S33: -0.0070 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 327 A 490 REMARK 3 ORIGIN FOR THE GROUP (A): -33.1679 12.9066 -8.9207 REMARK 3 T TENSOR REMARK 3 T11: 0.0606 T22: 0.0699 REMARK 3 T33: 0.0715 T12: -0.0010 REMARK 3 T13: 0.0008 T23: 0.0122 REMARK 3 L TENSOR REMARK 3 L11: 0.5079 L22: 0.9131 REMARK 3 L33: 0.7989 L12: -0.0590 REMARK 3 L13: -0.0823 L23: 0.5288 REMARK 3 S TENSOR REMARK 3 S11: -0.0059 S12: 0.0341 S13: 0.0432 REMARK 3 S21: -0.0625 S22: -0.0038 S23: 0.1356 REMARK 3 S31: -0.0312 S32: -0.1328 S33: 0.0098 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS. REMARK 4 REMARK 4 4C13 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 09-AUG-13. REMARK 100 THE DEPOSITION ID IS D_1290057963. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-JAN-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : SEALED TUBE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : XENOCS GENIX 3D CU HF REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MAR SCANNER 345 MM PLATE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 44765 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 41.700 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.9 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : 0.08000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 8.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.1 REMARK 200 DATA REDUNDANCY IN SHELL : 3.80 REMARK 200 R MERGE FOR SHELL (I) : 0.44000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.700 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: NONE REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.15 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.74 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: MORPHEUS SCREEN CONDITION C5 (0.1 M NA REMARK 280 HEPES/MOPS PH 7.5, 0.09 M NITRATE PHOSPHATE SULPHATE MIX, 30 % REMARK 280 (W/V) PEG550MME/PEG20K MIX) 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 78.91000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 27.01500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 78.91000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 27.01500 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5730 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 35520 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -86.0 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 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 0.00000 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 PRO A 491 REMARK 465 VAL A 492 REMARK 465 ASP A 493 REMARK 465 ARG A 494 REMARK 465 SER A 495 REMARK 465 HIS A 496 REMARK 465 HIS A 497 REMARK 465 HIS A 498 REMARK 465 HIS A 499 REMARK 465 HIS A 500 REMARK 465 HIS A 501 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 20 CG CD OE1 OE2 REMARK 470 GLN A 54 CG CD OE1 NE2 REMARK 470 LYS A 130 CE NZ REMARK 470 ASN A 328 CG OD1 ND2 REMARK 470 LYS A 370 CG CD CE NZ REMARK 470 GLN A 427 CG CD OE1 NE2 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 HIS A 50 CG HIS A 50 CD2 0.058 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 LYS A 51 -18.49 -49.97 REMARK 500 ASN A 143 -108.14 50.97 REMARK 500 SER A 199 -68.24 -99.81 REMARK 500 ILE A 261 -53.87 -121.59 REMARK 500 LEU A 336 60.59 26.38 REMARK 500 ASP A 340 95.12 -9.59 REMARK 500 HIS A 353 18.28 -149.59 REMARK 500 GLN A 371 -109.14 -126.94 REMARK 500 ALA A 409 -124.53 52.86 REMARK 500 SER A 456 -9.78 116.39 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 K A 605 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER A 100 O REMARK 620 2 LEU A 103 O 89.2 REMARK 620 3 THR A 105 OG1 103.3 106.2 REMARK 620 4 ASP A 194 OD2 176.7 88.8 79.7 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 503 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR A 115 OG1 REMARK 620 2 THR A 137 OG1 85.6 REMARK 620 3 GLU A 177 OE1 78.7 80.0 REMARK 620 4 PO4 A 601 O4 88.1 154.6 122.8 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 504 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 KCX A 219 OQ1 REMARK 620 2 HOH A2042 O 78.6 REMARK 620 N 1 REMARK 630 REMARK 630 MOLECULE TYPE: GLYCOPEPTIDE METABOLISM REMARK 630 MOLECULE NAME: URIDINE 5'DIPHOSPHO N-ACETYL MURAMOYL-L-ALANYL-D- REMARK 630 GLUTAMYL-L-LYSINE REMARK 630 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 630 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 630 REMARK 630 M RES C SSSEQI REMARK 630 UML A 598 REMARK 630 SOURCE: NULL REMARK 630 TAXONOMY: NULL REMARK 630 SUBCOMP: UDP MUB ALA DGL LYS REMARK 630 DETAILS: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE UML A 598 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 A 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 504 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE K A 605 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4C12 RELATED DB: PDB REMARK 900 X-RAY CRYSTAL STRUCTURE OF STAPHYLOCOCCUS AUREUS MURE WITH UDP- REMARK 900 MURNAC-ALA-GLU-LYS AND ADP REMARK 999 REMARK 999 SEQUENCE REMARK 999 AN ARG-SER-HIS6 ON THE C-TERMINUS DBREF 4C13 A 1 493 UNP D4U2M7 D4U2M7_STAAU 1 493 SEQADV 4C13 ARG A 494 UNP D4U2M7 EXPRESSION TAG SEQADV 4C13 SER A 495 UNP D4U2M7 EXPRESSION TAG SEQADV 4C13 HIS A 496 UNP D4U2M7 EXPRESSION TAG SEQADV 4C13 HIS A 497 UNP D4U2M7 EXPRESSION TAG SEQADV 4C13 HIS A 498 UNP D4U2M7 EXPRESSION TAG SEQADV 4C13 HIS A 499 UNP D4U2M7 EXPRESSION TAG SEQADV 4C13 HIS A 500 UNP D4U2M7 EXPRESSION TAG SEQADV 4C13 HIS A 501 UNP D4U2M7 EXPRESSION TAG SEQRES 1 A 501 MET ASP ALA SER THR LEU PHE LYS LYS VAL LYS VAL LYS SEQRES 2 A 501 ARG VAL LEU GLY SER LEU GLU GLN GLN ILE ASP ASP ILE SEQRES 3 A 501 THR THR ASP SER ARG THR ALA ARG GLU GLY SER ILE PHE SEQRES 4 A 501 VAL ALA SER VAL GLY TYR THR VAL ASP SER HIS LYS PHE SEQRES 5 A 501 CYS GLN ASN VAL ALA ASP GLN GLY CYS LYS LEU VAL VAL SEQRES 6 A 501 VAL ASN LYS GLU GLN SER LEU PRO ALA ASN VAL THR GLN SEQRES 7 A 501 VAL VAL VAL PRO ASP THR LEU ARG VAL ALA SER ILE LEU SEQRES 8 A 501 ALA HIS THR LEU TYR ASP TYR PRO SER HIS GLN LEU VAL SEQRES 9 A 501 THR PHE GLY VAL THR GLY THR ASN GLY LYS THR SER ILE SEQRES 10 A 501 ALA THR MET ILE HIS LEU ILE GLN ARG LYS LEU GLN LYS SEQRES 11 A 501 ASN SER ALA TYR LEU GLY THR ASN GLY PHE GLN ILE ASN SEQRES 12 A 501 GLU THR LYS THR LYS GLY ALA ASN THR THR PRO GLU THR SEQRES 13 A 501 VAL SER LEU THR LYS LYS ILE LYS GLU ALA VAL ASP ALA SEQRES 14 A 501 GLY ALA GLU SER MET THR LEU GLU VAL SER SER HIS GLY SEQRES 15 A 501 LEU VAL LEU GLY ARG LEU ARG GLY VAL GLU PHE ASP VAL SEQRES 16 A 501 ALA ILE PHE SER ASN LEU THR GLN ASP HIS LEU ASP PHE SEQRES 17 A 501 HIS GLY THR MET GLU ALA TYR GLY HIS ALA KCX SER LEU SEQRES 18 A 501 LEU PHE SER GLN LEU GLY GLU ASP LEU SER LYS GLU LYS SEQRES 19 A 501 TYR VAL VAL LEU ASN ASN ASP ASP SER PHE SER GLU TYR SEQRES 20 A 501 LEU ARG THR VAL THR PRO TYR GLU VAL PHE SER TYR GLY SEQRES 21 A 501 ILE ASP GLU GLU ALA GLN PHE MET ALA LYS ASN ILE GLN SEQRES 22 A 501 GLU SER LEU GLN GLY VAL SER PHE ASP PHE VAL THR PRO SEQRES 23 A 501 PHE GLY THR TYR PRO VAL LYS SER PRO TYR VAL GLY LYS SEQRES 24 A 501 PHE ASN ILE SER ASN ILE MET ALA ALA MET ILE ALA VAL SEQRES 25 A 501 TRP SER LYS GLY THR SER LEU GLU THR ILE ILE LYS ALA SEQRES 26 A 501 VAL GLU ASN LEU GLU PRO VAL GLU GLY ARG LEU GLU VAL SEQRES 27 A 501 LEU ASP PRO SER LEU PRO ILE ASP LEU ILE ILE ASP TYR SEQRES 28 A 501 ALA HIS THR ALA ASP GLY MET ASN LYS LEU ILE ASP ALA SEQRES 29 A 501 VAL GLN PRO PHE VAL LYS GLN LYS LEU ILE PHE LEU VAL SEQRES 30 A 501 GLY MET ALA GLY GLU ARG ASP LEU THR LYS THR PRO GLU SEQRES 31 A 501 MET GLY ARG VAL ALA CYS ARG ALA ASP TYR VAL ILE PHE SEQRES 32 A 501 THR PRO ASP ASN PRO ALA ASN ASP ASP PRO LYS MET LEU SEQRES 33 A 501 THR ALA GLU LEU ALA LYS GLY ALA THR HIS GLN ASN TYR SEQRES 34 A 501 ILE GLU PHE ASP ASP ARG ALA GLU GLY ILE LYS HIS ALA SEQRES 35 A 501 ILE ASP ILE ALA GLU PRO GLY ASP THR VAL VAL LEU ALA SEQRES 36 A 501 SER LYS GLY ARG GLU PRO TYR GLN ILE MET PRO GLY HIS SEQRES 37 A 501 ILE LYS VAL PRO HIS ARG ASP ASP LEU ILE GLY LEU GLU SEQRES 38 A 501 ALA ALA TYR LYS LYS PHE GLY GLY GLY PRO VAL ASP ARG SEQRES 39 A 501 SER HIS HIS HIS HIS HIS HIS MODRES 4C13 KCX A 219 LYS LYSINE NZ-CARBOXYLIC ACID HET KCX A 219 12 HET CL A 502 1 HET MG A 503 1 HET MG A 504 1 HET UML A 598 67 HET PO4 A 601 5 HET K A 605 1 HETNAM KCX LYSINE NZ-CARBOXYLIC ACID HETNAM CL CHLORIDE ION HETNAM MG MAGNESIUM ION HETNAM UML URIDINE 5'DIPHOSPHO N-ACETYL MURAMOYL-L-ALANYL-D- HETNAM 2 UML GLUTAMYL-L-LYSINE HETNAM PO4 PHOSPHATE ION HETNAM K POTASSIUM ION FORMUL 1 KCX C7 H14 N2 O4 FORMUL 2 CL CL 1- FORMUL 3 MG 2(MG 2+) FORMUL 5 UML C34 H55 N7 O24 P2 FORMUL 6 PO4 O4 P 3- FORMUL 7 K K 1+ FORMUL 8 HOH *213(H2 O) HELIX 1 1 ASP A 2 LYS A 8 1 7 HELIX 2 2 ASP A 29 ALA A 33 5 5 HELIX 3 3 SER A 49 LYS A 51 5 3 HELIX 4 4 PHE A 52 GLN A 59 1 8 HELIX 5 5 ASP A 83 TYR A 96 1 14 HELIX 6 6 TYR A 98 GLN A 102 5 5 HELIX 7 7 GLY A 113 LEU A 128 1 16 HELIX 8 8 GLU A 155 ALA A 169 1 15 HELIX 9 9 SER A 179 LEU A 185 1 7 HELIX 10 10 HIS A 205 GLY A 210 1 6 HELIX 11 11 THR A 211 GLN A 225 1 15 HELIX 12 12 PHE A 244 THR A 250 1 7 HELIX 13 13 GLY A 298 LYS A 315 1 18 HELIX 14 14 SER A 318 GLU A 327 1 10 HELIX 15 15 THR A 354 GLN A 366 1 13 HELIX 16 16 PRO A 367 VAL A 369 5 3 HELIX 17 17 LYS A 387 CYS A 396 1 10 HELIX 18 18 ASP A 412 LYS A 422 1 11 HELIX 19 19 ASP A 434 ALA A 446 1 13 HELIX 20 20 PRO A 466 HIS A 468 5 3 HELIX 21 21 ARG A 474 GLY A 488 1 15 SHEET 1 AA 5 ARG A 14 LEU A 16 0 SHEET 2 AA 5 THR A 77 VAL A 80 -1 O GLN A 78 N LEU A 16 SHEET 3 AA 5 LEU A 63 VAL A 66 1 O VAL A 64 N VAL A 79 SHEET 4 AA 5 SER A 37 VAL A 40 1 O PHE A 39 N VAL A 65 SHEET 5 AA 5 ASP A 25 THR A 27 1 O ASP A 25 N ILE A 38 SHEET 1 AB11 THR A 145 THR A 147 0 SHEET 2 AB11 GLY A 139 ILE A 142 -1 O PHE A 140 N THR A 147 SHEET 3 AB11 SER A 132 GLY A 136 -1 O TYR A 134 N GLN A 141 SHEET 4 AB11 SER A 173 GLU A 177 1 O SER A 173 N ALA A 133 SHEET 5 AB11 VAL A 104 THR A 109 1 O VAL A 104 N MET A 174 SHEET 6 AB11 VAL A 195 PHE A 198 1 O VAL A 195 N GLY A 107 SHEET 7 AB11 TYR A 235 ASN A 239 1 O TYR A 235 N ALA A 196 SHEET 8 AB11 GLU A 255 GLY A 260 1 O GLU A 255 N VAL A 236 SHEET 9 AB11 PHE A 267 SER A 275 1 O PHE A 267 N GLY A 260 SHEET 10 AB11 GLY A 278 THR A 285 -1 O GLY A 278 N SER A 275 SHEET 11 AB11 GLY A 288 SER A 294 -1 O GLY A 288 N THR A 285 SHEET 1 AC 6 GLU A 337 VAL A 338 0 SHEET 2 AC 6 ASP A 346 ASP A 350 -1 O ILE A 349 N GLU A 337 SHEET 3 AC 6 THR A 451 ALA A 455 1 O VAL A 452 N ILE A 348 SHEET 4 AC 6 LEU A 373 ALA A 380 1 O ILE A 374 N VAL A 453 SHEET 5 AC 6 TYR A 400 ASP A 406 1 O TYR A 400 N PHE A 375 SHEET 6 AC 6 TYR A 429 GLU A 431 1 O ILE A 430 N PHE A 403 SHEET 1 AD 2 TYR A 462 MET A 465 0 SHEET 2 AD 2 ILE A 469 PRO A 472 -1 O ILE A 469 N MET A 465 LINK C ALA A 218 N KCX A 219 1555 1555 1.33 LINK C KCX A 219 N SER A 220 1555 1555 1.35 LINK O SER A 100 K K A 605 1555 1555 2.42 LINK O LEU A 103 K K A 605 1555 1555 2.50 LINK OG1 THR A 105 K K A 605 1555 1555 2.66 LINK OG1 THR A 115 MG MG A 503 1555 1555 2.52 LINK OG1 THR A 137 MG MG A 503 1555 1555 2.49 LINK OE1 GLU A 177 MG MG A 503 1555 1555 2.26 LINK OD2 ASP A 194 K K A 605 1555 1555 2.49 LINK OQ1 KCX A 219 MG MG A 504 1555 1555 2.72 LINK MG MG A 503 O4 PO4 A 601 1555 1555 2.52 LINK MG MG A 504 O HOH A2042 1555 1555 2.94 SITE 1 AC1 35 THR A 28 ASP A 29 SER A 30 ARG A 31 SITE 2 AC1 35 GLY A 44 TYR A 45 THR A 46 VAL A 47 SITE 3 AC1 35 SER A 49 PHE A 52 ASN A 151 THR A 152 SITE 4 AC1 35 THR A 153 GLU A 155 SER A 179 HIS A 181 SITE 5 AC1 35 ARG A 187 HIS A 205 TYR A 351 ARG A 383 SITE 6 AC1 35 ASP A 406 ASN A 407 SER A 456 GLU A 460 SITE 7 AC1 35 HOH A2017 HOH A2070 HOH A2071 HOH A2093 SITE 8 AC1 35 HOH A2103 HOH A2188 HOH A2209 HOH A2210 SITE 9 AC1 35 HOH A2211 HOH A2212 HOH A2213 SITE 1 AC2 10 ASN A 112 GLY A 113 LYS A 114 THR A 115 SITE 2 AC2 10 SER A 116 ARG A 335 TYR A 351 MG A 503 SITE 3 AC2 10 HOH A2039 HOH A2043 SITE 1 AC3 1 SER A 258 SITE 1 AC4 4 THR A 115 THR A 137 GLU A 177 PO4 A 601 SITE 1 AC5 5 THR A 111 LYS A 114 HIS A 205 KCX A 219 SITE 2 AC5 5 HOH A2042 SITE 1 AC6 4 SER A 100 LEU A 103 THR A 105 ASP A 194 CRYST1 157.820 54.030 70.970 90.00 92.02 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 0.006336 0.000000 0.000223 0.00000 SCALE2 0.000000 0.018508 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014099 0.00000