HEADER LIGASE 17-JUN-15 5A5E TITLE CRYSTAL STRUCTURE OF MURD LIGASE FROM ESCHERICHIA COLI COMPND MOL_ID: 1; COMPND 2 MOLECULE: UDP-N-ACETYLMURAMOYLALANINE--D-GLUTAMATE LIGASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: D-GLUTAMIC ACID-ADDING ENZYME, UDP-N-ACETYLMURAMOYL-L-ALANY COMPND 5 L-D-GLUTAMATE SYNTHETASE, MURD LIGASE; COMPND 6 EC: 6.3.2.9; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI K-12; SOURCE 3 ORGANISM_TAXID: 83333; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI DH5[ALPHA]; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 668369 KEYWDS LIGASE, PEPTIDOGLYCAN SYNTHESIS, ADP-FORMING ENZYME, CELL WALL, CELL KEYWDS 2 SHAPE, CELL CYCLE, NUCLEOTIDE-BINDING, ATP- BINDING, CELL DIVISION, KEYWDS 3 LIGAND, CONFORMATION EXPDTA X-RAY DIFFRACTION AUTHOR R.SINK,M.KOTNIK,A.ZEGA,H.BARRETEAU,S.GOBEC,D.BLANOT,A.DESSEN, AUTHOR 2 C.CONTRERAS-MARTEL REVDAT 4 10-JAN-24 5A5E 1 REMARK LINK REVDAT 3 13-MAR-19 5A5E 1 REMARK REVDAT 2 28-FEB-18 5A5E 1 SOURCE JRNL REVDAT 1 13-APR-16 5A5E 0 JRNL AUTH R.SINK,M.KOTNIK,A.ZEGA,H.BARRETEAU,S.GOBEC,D.BLANOT, JRNL AUTH 2 A.DESSEN,C.CONTRERAS-MARTEL JRNL TITL CRYSTALLOGRAPHIC STUDY OF PEPTIDOGLYCAN BIOSYNTHESIS ENZYME JRNL TITL 2 MURD: DOMAIN MOVEMENT REVISITED. JRNL REF PLOS ONE V. 11 52075 2016 JRNL REFN ESSN 1932-6203 JRNL PMID 27031227 JRNL DOI 10.1371/JOURNAL.PONE.0152075 REMARK 2 REMARK 2 RESOLUTION. 1.84 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.7.0032 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) : 1.84 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.83 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 95.1 REMARK 3 NUMBER OF REFLECTIONS : 33040 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) : 0.191 REMARK 3 R VALUE (WORKING SET) : 0.189 REMARK 3 FREE R VALUE : 0.231 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 1720 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) : 1.84 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.89 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2466 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.56 REMARK 3 BIN R VALUE (WORKING SET) : 0.2910 REMARK 3 BIN FREE R VALUE SET COUNT : 116 REMARK 3 BIN FREE R VALUE : 0.3220 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3232 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 39 REMARK 3 SOLVENT ATOMS : 297 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 26.88 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 24.00 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.45000 REMARK 3 B22 (A**2) : 1.53000 REMARK 3 B33 (A**2) : -1.08000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.158 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.145 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.101 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 6.359 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.953 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.929 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3349 ; 0.010 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4557 ; 1.537 ; 1.982 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 439 ; 5.657 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 143 ;36.535 ;24.476 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 550 ;12.183 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 22 ;13.547 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 532 ; 0.125 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2515 ; 0.010 ; 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): 1732 ; 1.357 ; 1.181 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2164 ; 1.952 ; 1.762 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1617 ; 2.611 ; 1.493 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 : 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 92 REMARK 3 ORIGIN FOR THE GROUP (A): -4.3541 55.8312 48.0966 REMARK 3 T TENSOR REMARK 3 T11: 0.1146 T22: 0.0901 REMARK 3 T33: 0.0446 T12: 0.0288 REMARK 3 T13: 0.0121 T23: -0.0043 REMARK 3 L TENSOR REMARK 3 L11: 1.8504 L22: 3.5442 REMARK 3 L33: 3.6518 L12: 0.8424 REMARK 3 L13: 1.0149 L23: -0.8669 REMARK 3 S TENSOR REMARK 3 S11: -0.0119 S12: -0.1263 S13: -0.0599 REMARK 3 S21: 0.1954 S22: 0.0409 S23: -0.2184 REMARK 3 S31: -0.0046 S32: 0.0568 S33: -0.0290 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 94 A 295 REMARK 3 ORIGIN FOR THE GROUP (A): -0.5514 47.1427 19.2887 REMARK 3 T TENSOR REMARK 3 T11: 0.0095 T22: 0.0150 REMARK 3 T33: 0.0456 T12: -0.0032 REMARK 3 T13: -0.0169 T23: 0.0105 REMARK 3 L TENSOR REMARK 3 L11: 1.3496 L22: 1.3853 REMARK 3 L33: 2.4990 L12: -0.2350 REMARK 3 L13: -0.8288 L23: 0.6396 REMARK 3 S TENSOR REMARK 3 S11: -0.0142 S12: 0.0165 S13: -0.0525 REMARK 3 S21: 0.0123 S22: 0.0222 S23: -0.0544 REMARK 3 S31: 0.0807 S32: 0.0683 S33: -0.0080 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 304 A 439 REMARK 3 ORIGIN FOR THE GROUP (A): 27.1896 51.3331 20.5146 REMARK 3 T TENSOR REMARK 3 T11: 0.0132 T22: 0.0650 REMARK 3 T33: 0.0632 T12: -0.0091 REMARK 3 T13: -0.0012 T23: 0.0108 REMARK 3 L TENSOR REMARK 3 L11: 2.8717 L22: 1.3226 REMARK 3 L33: 2.6818 L12: -0.4526 REMARK 3 L13: 0.1151 L23: -0.1518 REMARK 3 S TENSOR REMARK 3 S11: 0.0156 S12: 0.0214 S13: -0.1235 REMARK 3 S21: 0.0082 S22: 0.0014 S23: 0.0255 REMARK 3 S31: 0.0784 S32: -0.0756 S33: -0.0170 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH 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 5A5E COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 17-JUN-15. REMARK 100 THE DEPOSITION ID IS D_1290064090. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-APR-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : BM14 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97624 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 34760 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.840 REMARK 200 RESOLUTION RANGE LOW (A) : 44.830 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.1 REMARK 200 DATA REDUNDANCY : 4.200 REMARK 200 R MERGE (I) : 0.06000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 22.7400 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.84 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.95 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.3 REMARK 200 DATA REDUNDANCY IN SHELL : 4.40 REMARK 200 R MERGE FOR SHELL (I) : 0.50000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.010 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 3UAG REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.64 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.14 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 3 MG/ML PROTEIN, 1.8 M (NH4)2SO4, 7% REMARK 280 MPD, 0.1 M MES, PH 5.6, 15C, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 288K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 29.06000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 50.29050 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 35.21650 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 50.29050 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 29.06000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 35.21650 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 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 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 GLU A 181 REMARK 465 ASP A 182 REMARK 465 HIS A 183 REMARK 465 MET A 184 REMARK 465 ASP A 185 REMARK 465 ARG A 186 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 SER A 56 170.48 179.95 REMARK 500 GLN A 243 97.26 -1.81 REMARK 500 HIS A 301 -0.20 79.10 REMARK 500 ARG A 357 -36.31 -38.53 REMARK 500 ARG A 380 81.54 -159.88 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 NI A 650 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 253 OE2 REMARK 620 2 HIS A 309 ND1 137.0 REMARK 620 3 HIS A 309 ND1 106.1 81.7 REMARK 620 N 1 2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MPD A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NI A 650 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 800 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 801 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 802 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 803 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 804 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1441 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5A5F RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF MURD LIGASE FROM ESCHERICHIA COLI IN COMPLEX REMARK 900 WITH UMA AND ADP DBREF 5A5E A 1 437 UNP P14900 MURD_ECOLI 2 438 SEQRES 1 A 437 ALA ASP TYR GLN GLY LYS ASN VAL VAL ILE ILE GLY LEU SEQRES 2 A 437 GLY LEU THR GLY LEU SER CYS VAL ASP PHE PHE LEU ALA SEQRES 3 A 437 ARG GLY VAL THR PRO ARG VAL MET ASP THR ARG MET THR SEQRES 4 A 437 PRO PRO GLY LEU ASP LYS LEU PRO GLU ALA VAL GLU ARG SEQRES 5 A 437 HIS THR GLY SER LEU ASN ASP GLU TRP LEU MET ALA ALA SEQRES 6 A 437 ASP LEU ILE VAL ALA SER PRO GLY ILE ALA LEU ALA HIS SEQRES 7 A 437 PRO SER LEU SER ALA ALA ALA ASP ALA GLY ILE GLU ILE SEQRES 8 A 437 VAL GLY ASP ILE GLU LEU PHE CYS ARG GLU ALA GLN ALA SEQRES 9 A 437 PRO ILE VAL ALA ILE THR GLY SER ASN GLY LYS SER THR SEQRES 10 A 437 VAL THR THR LEU VAL GLY GLU MET ALA LYS ALA ALA GLY SEQRES 11 A 437 VAL ASN VAL GLY VAL GLY GLY ASN ILE GLY LEU PRO ALA SEQRES 12 A 437 LEU MET LEU LEU ASP ASP GLU CYS GLU LEU TYR VAL LEU SEQRES 13 A 437 GLU LEU SER SER PHE GLN LEU GLU THR THR SER SER LEU SEQRES 14 A 437 GLN ALA VAL ALA ALA THR ILE LEU ASN VAL THR GLU ASP SEQRES 15 A 437 HIS MET ASP ARG TYR PRO PHE GLY LEU GLN GLN TYR ARG SEQRES 16 A 437 ALA ALA LYS LEU ARG ILE TYR GLU ASN ALA LYS VAL CYS SEQRES 17 A 437 VAL VAL ASN ALA ASP ASP ALA LEU THR MET PRO ILE ARG SEQRES 18 A 437 GLY ALA ASP GLU ARG CYS VAL SER PHE GLY VAL ASN MET SEQRES 19 A 437 GLY ASP TYR HIS LEU ASN HIS GLN GLN GLY GLU THR TRP SEQRES 20 A 437 LEU ARG VAL LYS GLY GLU LYS VAL LEU ASN VAL LYS GLU SEQRES 21 A 437 MET LYS LEU SER GLY GLN HIS ASN TYR THR ASN ALA LEU SEQRES 22 A 437 ALA ALA LEU ALA LEU ALA ASP ALA ALA GLY LEU PRO ARG SEQRES 23 A 437 ALA SER SER LEU LYS ALA LEU THR THR PHE THR GLY LEU SEQRES 24 A 437 PRO HIS ARG PHE GLU VAL VAL LEU GLU HIS ASN GLY VAL SEQRES 25 A 437 ARG TRP ILE ASN ASP SER LYS ALA THR ASN VAL GLY SER SEQRES 26 A 437 THR GLU ALA ALA LEU ASN GLY LEU HIS VAL ASP GLY THR SEQRES 27 A 437 LEU HIS LEU LEU LEU GLY GLY ASP GLY LYS SER ALA ASP SEQRES 28 A 437 PHE SER PRO LEU ALA ARG TYR LEU ASN GLY ASP ASN VAL SEQRES 29 A 437 ARG LEU TYR CYS PHE GLY ARG ASP GLY ALA GLN LEU ALA SEQRES 30 A 437 ALA LEU ARG PRO GLU VAL ALA GLU GLN THR GLU THR MET SEQRES 31 A 437 GLU GLN ALA MET ARG LEU LEU ALA PRO ARG VAL GLN PRO SEQRES 32 A 437 GLY ASP MET VAL LEU LEU SER PRO ALA CYS ALA SER LEU SEQRES 33 A 437 ASP GLN PHE LYS ASN PHE GLU GLN ARG GLY ASN GLU PHE SEQRES 34 A 437 ALA ARG LEU ALA LYS GLU LEU GLY HET MPD A 502 8 HET NI A 650 1 HET SO4 A 800 5 HET SO4 A 801 5 HET SO4 A 802 5 HET SO4 A 803 5 HET SO4 A 804 5 HET SO4 A1441 5 HETNAM MPD (4S)-2-METHYL-2,4-PENTANEDIOL HETNAM NI NICKEL (II) ION HETNAM SO4 SULFATE ION FORMUL 2 MPD C6 H14 O2 FORMUL 3 NI NI 2+ FORMUL 4 SO4 6(O4 S 2-) FORMUL 10 HOH *297(H2 O) HELIX 1 1 GLY A 14 ARG A 27 1 14 HELIX 2 2 PRO A 40 LEU A 46 5 7 HELIX 3 3 ASN A 58 ALA A 65 1 8 HELIX 4 4 GLY A 73 ALA A 77 5 5 HELIX 5 5 HIS A 78 ALA A 87 1 10 HELIX 6 6 GLY A 93 ALA A 102 1 10 HELIX 7 7 GLY A 114 ALA A 129 1 16 HELIX 8 8 PRO A 142 LEU A 147 5 6 HELIX 9 9 SER A 159 THR A 165 1 7 HELIX 10 10 GLY A 190 ARG A 200 1 11 HELIX 11 11 ILE A 201 GLU A 203 5 3 HELIX 12 12 ASP A 214 MET A 218 5 5 HELIX 13 13 LYS A 259 MET A 261 5 3 HELIX 14 14 GLY A 265 ALA A 282 1 18 HELIX 15 15 PRO A 285 PHE A 296 1 12 HELIX 16 16 ASN A 322 ASN A 331 1 10 HELIX 17 17 PHE A 352 LEU A 359 5 8 HELIX 18 18 ASP A 372 ALA A 378 1 7 HELIX 19 19 LEU A 379 GLU A 382 5 4 HELIX 20 20 THR A 389 ALA A 398 1 10 HELIX 21 21 PRO A 399 VAL A 401 5 3 HELIX 22 22 ASN A 421 GLY A 437 1 17 SHEET 1 AA 5 ARG A 52 THR A 54 0 SHEET 2 AA 5 ARG A 32 ASP A 35 1 O VAL A 33 N HIS A 53 SHEET 3 AA 5 VAL A 8 ILE A 11 1 O VAL A 8 N ARG A 32 SHEET 4 AA 5 LEU A 67 ALA A 70 1 O LEU A 67 N VAL A 9 SHEET 5 AA 5 GLU A 90 VAL A 92 1 O GLU A 90 N ILE A 68 SHEET 1 AB 6 VAL A 133 GLY A 137 0 SHEET 2 AB 6 LEU A 153 GLU A 157 1 O LEU A 153 N GLY A 134 SHEET 3 AB 6 ILE A 106 THR A 110 1 O VAL A 107 N LEU A 156 SHEET 4 AB 6 ALA A 173 ILE A 176 1 O ALA A 173 N ALA A 108 SHEET 5 AB 6 VAL A 207 ASN A 211 1 O VAL A 207 N ALA A 174 SHEET 6 AB 6 CYS A 227 PHE A 230 1 O VAL A 228 N VAL A 210 SHEET 1 AC 3 TYR A 237 GLN A 242 0 SHEET 2 AC 3 GLU A 245 VAL A 250 -1 O GLU A 245 N GLN A 242 SHEET 3 AC 3 GLU A 253 ASN A 257 -1 O GLU A 253 N VAL A 250 SHEET 1 AD 6 GLU A 304 HIS A 309 0 SHEET 2 AD 6 VAL A 312 ASN A 316 -1 O VAL A 312 N HIS A 309 SHEET 3 AD 6 MET A 406 LEU A 409 1 O VAL A 407 N ILE A 315 SHEET 4 AD 6 LEU A 339 GLY A 344 1 O HIS A 340 N LEU A 408 SHEET 5 AD 6 VAL A 364 PHE A 369 1 O ARG A 365 N LEU A 341 SHEET 6 AD 6 ALA A 384 GLN A 386 1 O GLU A 385 N CYS A 368 SSBOND 1 CYS A 208 CYS A 227 1555 1555 2.03 LINK OE2 GLU A 253 NI NI A 650 4565 1555 2.10 LINK ND1BHIS A 309 NI NI A 650 1555 1555 1.95 LINK ND1AHIS A 309 NI NI A 650 1555 1555 1.87 SITE 1 AC1 5 LEU A 15 ALA A 212 MET A 218 SER A 229 SITE 2 AC1 5 HOH A2020 SITE 1 AC2 2 GLU A 253 HIS A 309 SITE 1 AC3 7 GLY A 111 LYS A 115 SER A 160 TYR A 194 SITE 2 AC3 7 LYS A 198 HOH A2109 HOH A2124 SITE 1 AC4 7 THR A 321 ALA A 414 SER A 415 LEU A 416 SITE 2 AC4 7 ASN A 421 PHE A 422 HOH A2297 SITE 1 AC5 5 SER A 264 GLY A 265 TYR A 269 HIS A 334 SITE 2 AC5 5 HOH A2192 SITE 1 AC6 3 ALA A 282 GLY A 283 ARG A 400 SITE 1 AC7 6 GLY A 14 LEU A 15 THR A 16 HOH A2010 SITE 2 AC7 6 HOH A2011 HOH A2059 SITE 1 AC8 8 GLY A 114 LYS A 115 SER A 116 THR A 117 SITE 2 AC8 8 ARG A 302 LYS A 319 HOH A2096 HOH A2234 CRYST1 58.120 70.433 100.581 90.00 90.00 90.00 P 21 21 21 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 0.017206 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014198 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009942 0.00000