HEADER LIGASE 09-AUG-13 4C12 TITLE X-RAY CRYSTAL STRUCTURE OF STAPHYLOCOCCUS AUREUS MURE WITH UDP-MURNAC- TITLE 2 ALA-GLU-LYS AND ADP 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 EXPDTA X-RAY DIFFRACTION AUTHOR V.FULOP,D.I.ROPER,K.M.RUANE,H.BARRETEAU,A.BONIFACE,S.DEMENTIN, AUTHOR 2 D.BLANOT,D.MENGIN-LECREULX,S.GOBEC,A.DESSEN,C.G.DOWSON,A.J.LLOYD REVDAT 4 20-DEC-23 4C12 1 REMARK LINK REVDAT 3 27-NOV-13 4C12 1 JRNL REVDAT 2 09-OCT-13 4C12 1 JRNL REVDAT 1 02-OCT-13 4C12 0 JRNL AUTH K.M.RUANE,A.J.LLOYD,V.FULOP,C.G.DOWSON,H.BARRETEAU, JRNL AUTH 2 A.BONIFACE,S.DEMENTIN,D.BLANOT,D.MENGIN-LECREULX,S.GOBEC, JRNL AUTH 3 A.DESSEN,D.I.ROPER JRNL TITL SPECIFICITY DETERMINANTS FOR LYSINE INCORPORATION IN JRNL TITL 2 STAPHYLOCOCCUS AUREUS PEPTIDOGLYCAN AS REVEALED BY THE JRNL TITL 3 STRUCTURE OF A MURE ENZYME TERNARY COMPLEX. JRNL REF J.BIOL.CHEM. V. 288 33439 2013 JRNL REFN ISSN 0021-9258 JRNL PMID 24064214 JRNL DOI 10.1074/JBC.M113.508135 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0109 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 52.23 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 88.9 REMARK 3 NUMBER OF REFLECTIONS : 48057 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) : 0.162 REMARK 3 R VALUE (WORKING SET) : 0.160 REMARK 3 FREE R VALUE : 0.197 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2065 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) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.85 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1981 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 49.99 REMARK 3 BIN R VALUE (WORKING SET) : 0.2580 REMARK 3 BIN FREE R VALUE SET COUNT : 86 REMARK 3 BIN FREE R VALUE : 0.2900 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3810 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 108 REMARK 3 SOLVENT ATOMS : 490 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.01 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.38000 REMARK 3 B22 (A**2) : -0.15000 REMARK 3 B33 (A**2) : -0.23000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.07000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.116 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.113 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.071 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.862 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.962 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.946 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3990 ; 0.015 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5417 ; 1.540 ; 1.995 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 492 ; 5.929 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 169 ;35.860 ;25.207 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 674 ;13.561 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 15 ;19.689 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 626 ; 0.119 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2954 ; 0.007 ; 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): 2450 ; 0.715 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3970 ; 1.230 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1540 ; 2.252 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1447 ; 3.605 ; 4.500 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 : 3 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 84 REMARK 3 ORIGIN FOR THE GROUP (A): 92.7700 11.7440 11.3610 REMARK 3 T TENSOR REMARK 3 T11: 0.0180 T22: 0.3228 REMARK 3 T33: 0.0741 T12: 0.0135 REMARK 3 T13: 0.0197 T23: -0.0477 REMARK 3 L TENSOR REMARK 3 L11: 1.8042 L22: 1.8453 REMARK 3 L33: 3.7763 L12: 0.7320 REMARK 3 L13: 0.7953 L23: 1.1534 REMARK 3 S TENSOR REMARK 3 S11: -0.0409 S12: 0.5069 S13: -0.1452 REMARK 3 S21: -0.1061 S22: 0.2373 S23: -0.1191 REMARK 3 S31: -0.0141 S32: 0.5284 S33: -0.1964 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 85 A 369 REMARK 3 ORIGIN FOR THE GROUP (A): 94.4720 19.4850 45.7340 REMARK 3 T TENSOR REMARK 3 T11: 0.0034 T22: 0.1005 REMARK 3 T33: 0.0965 T12: -0.0004 REMARK 3 T13: -0.0047 T23: -0.0045 REMARK 3 L TENSOR REMARK 3 L11: 1.1912 L22: 0.5043 REMARK 3 L33: 0.7911 L12: 0.0784 REMARK 3 L13: 0.6013 L23: -0.0079 REMARK 3 S TENSOR REMARK 3 S11: 0.0080 S12: -0.0878 S13: 0.0464 REMARK 3 S21: 0.0405 S22: -0.0282 S23: -0.0426 REMARK 3 S31: 0.0092 S32: 0.0051 S33: 0.0202 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 370 A 493 REMARK 3 ORIGIN FOR THE GROUP (A): 112.6890 38.6680 41.9900 REMARK 3 T TENSOR REMARK 3 T11: 0.0750 T22: 0.1202 REMARK 3 T33: 0.4469 T12: -0.0197 REMARK 3 T13: -0.0755 T23: 0.0723 REMARK 3 L TENSOR REMARK 3 L11: 1.6053 L22: 2.7035 REMARK 3 L33: 5.6483 L12: 0.0080 REMARK 3 L13: 0.4939 L23: -1.8731 REMARK 3 S TENSOR REMARK 3 S11: -0.2365 S12: 0.0578 S13: 0.1040 REMARK 3 S21: -0.0054 S22: -0.3995 S23: -0.6273 REMARK 3 S31: -0.3833 S32: 0.2076 S33: 0.6361 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 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 4C12 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_1290057970. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I02 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9795 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 50122 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 53.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 89.2 REMARK 200 DATA REDUNDANCY : 3.060 REMARK 200 R MERGE (I) : 0.07000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 11.1000 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) : 1.90 REMARK 200 COMPLETENESS FOR SHELL (%) : 54.9 REMARK 200 DATA REDUNDANCY IN SHELL : 2.80 REMARK 200 R MERGE FOR SHELL (I) : 0.39000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.500 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 1E8C REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.71 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.78 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: MORPHEUS SCREEN CONDITION D9 0.1 M REMARK 280 TRIS/BICINE, PH 8.5, 30% (W/V) PEG550MME/PEG20K MIX, 0.12 M 1,6 REMARK 280 HEXANEDIOL, 1-BUTANOL, 1,2-PROPANEDIOL (RACEMIC), 2-PROPANOL, 1, REMARK 280 4-BUTANEDIOL, 1,3-PROANEDIOL 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 79.27000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 27.14500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 79.27000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 27.14500 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: 6930 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 36480 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -69.8 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 156.55226 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 71.16224 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 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 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 OD2 ASP A 262 O HOH A 2307 2.13 REMARK 500 O HOH A 2321 O HOH A 2327 2.17 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG A 34 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 LEU A 63 CA - CB - CG ANGL. DEV. = 15.6 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 ASN A 143 -110.76 49.40 REMARK 500 SER A 199 -70.58 -97.14 REMARK 500 LEU A 336 67.72 27.45 REMARK 500 ASP A 340 91.77 -6.23 REMARK 500 GLN A 371 -101.02 -134.85 REMARK 500 ALA A 409 -118.16 52.50 REMARK 500 SER A 456 -14.62 119.40 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 A2087 DISTANCE = 6.21 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 MG A1501 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR A 111 O REMARK 620 2 KCX A 219 OQ2 103.5 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A1500 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR A 115 OG1 REMARK 620 2 THR A 137 OG1 94.6 REMARK 620 3 GLU A 177 OE1 82.5 87.3 REMARK 620 4 ADP A1499 O2B 79.5 161.5 109.0 REMARK 620 5 HOH A2152 O 75.4 91.1 157.6 70.4 REMARK 620 6 HOH A2181 O 161.0 73.1 110.8 107.5 90.0 REMARK 620 N 1 2 3 4 5 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 1498 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 1498 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ADP A 1499 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 1500 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 1501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 1494 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 1495 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4C13 RELATED DB: PDB REMARK 900 X-RAY CRYSTAL STRUCTURE OF STAPHYLOCOCCUS AUREUS MURE WITH UDP- REMARK 900 MURNAC-ALA-GLU-LYS DBREF 4C12 A 1 493 UNP Q2FZP6 MURE_STAA8 1 493 SEQADV 4C12 ARG A 494 UNP Q2FZP6 EXPRESSION TAG SEQADV 4C12 SER A 495 UNP Q2FZP6 EXPRESSION TAG SEQADV 4C12 HIS A 496 UNP Q2FZP6 EXPRESSION TAG SEQADV 4C12 HIS A 497 UNP Q2FZP6 EXPRESSION TAG SEQADV 4C12 HIS A 498 UNP Q2FZP6 EXPRESSION TAG SEQADV 4C12 HIS A 499 UNP Q2FZP6 EXPRESSION TAG SEQADV 4C12 HIS A 500 UNP Q2FZP6 EXPRESSION TAG SEQADV 4C12 HIS A 501 UNP Q2FZP6 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 4C12 KCX A 219 LYS LYSINE NZ-CARBOXYLIC ACID HET KCX A 219 12 HET GOL A1494 6 HET GOL A1495 6 HET UML A1498 67 HET ADP A1499 27 HET MG A1500 1 HET MG A1501 1 HETNAM KCX LYSINE NZ-CARBOXYLIC ACID HETNAM GOL GLYCEROL HETNAM UML URIDINE 5'DIPHOSPHO N-ACETYL MURAMOYL-L-ALANYL-D- HETNAM 2 UML GLUTAMYL-L-LYSINE HETNAM ADP ADENOSINE-5'-DIPHOSPHATE HETNAM MG MAGNESIUM ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 1 KCX C7 H14 N2 O4 FORMUL 2 GOL 2(C3 H8 O3) FORMUL 4 UML C34 H55 N7 O24 P2 FORMUL 5 ADP C10 H15 N5 O10 P2 FORMUL 6 MG 2(MG 2+) FORMUL 8 HOH *490(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 1.34 LINK C KCX A 219 N SER A 220 1555 1555 1.34 LINK O THR A 111 MG MG A1501 1555 1555 2.92 LINK OG1 THR A 115 MG MG A1500 1555 1555 2.41 LINK OG1 THR A 137 MG MG A1500 1555 1555 2.26 LINK OE1 GLU A 177 MG MG A1500 1555 1555 2.30 LINK OQ2 KCX A 219 MG MG A1501 1555 1555 2.71 LINK O2B ADP A1499 MG MG A1500 1555 1555 2.23 LINK MG MG A1500 O HOH A2152 1555 1555 2.54 LINK MG MG A1500 O HOH A2181 1555 1555 2.70 SITE 1 AC1 39 THR A 28 ASP A 29 SER A 30 ARG A 31 SITE 2 AC1 39 GLY A 44 TYR A 45 THR A 46 VAL A 47 SITE 3 AC1 39 SER A 49 PHE A 52 ASN A 151 THR A 152 SITE 4 AC1 39 THR A 153 GLU A 155 SER A 179 HIS A 181 SITE 5 AC1 39 ARG A 187 HIS A 205 TYR A 351 ARG A 383 SITE 6 AC1 39 ASP A 406 SER A 456 GLU A 460 HOH A2045 SITE 7 AC1 39 HOH A2049 HOH A2058 HOH A2206 HOH A2208 SITE 8 AC1 39 HOH A2396 HOH A2422 HOH A2479 HOH A2480 SITE 9 AC1 39 HOH A2481 HOH A2482 HOH A2483 HOH A2484 SITE 10 AC1 39 HOH A2485 HOH A2486 HOH A2487 SITE 1 AC2 24 THR A 111 ASN A 112 GLY A 113 LYS A 114 SITE 2 AC2 24 THR A 115 SER A 116 GLU A 177 ASN A 200 SITE 3 AC2 24 PHE A 300 ASN A 304 ARG A 335 ASP A 350 SITE 4 AC2 24 TYR A 351 ALA A 352 HIS A 353 ASP A 356 SITE 5 AC2 24 GLY A 357 LYS A 360 MG A1500 HOH A2143 SITE 6 AC2 24 HOH A2144 HOH A2152 HOH A2241 HOH A2488 SITE 1 AC3 6 THR A 115 THR A 137 GLU A 177 ADP A1499 SITE 2 AC3 6 HOH A2152 HOH A2181 SITE 1 AC4 5 THR A 111 LYS A 114 HIS A 205 KCX A 219 SITE 2 AC4 5 HOH A2151 SITE 1 AC5 4 MET A 212 GLU A 213 GOL A1495 HOH A2489 SITE 1 AC6 6 GLU A 213 HIS A 217 PHE A 244 TYR A 247 SITE 2 AC6 6 GOL A1494 HOH A2261 CRYST1 158.540 54.290 71.190 90.00 91.60 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 0.006308 0.000000 0.000176 0.00000 SCALE2 0.000000 0.018420 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014052 0.00000