HEADER LIGASE 17-JUN-15 5A5F TITLE CRYSTAL STRUCTURE OF MURD LIGASE FROM ESCHERICHIA COLI IN COMPLEX WITH TITLE 2 UMA AND ADP 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 3 10-JAN-24 5A5F 1 REMARK REVDAT 2 28-FEB-18 5A5F 1 SOURCE JRNL REVDAT 1 13-APR-16 5A5F 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. 1.90 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) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.47 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 3 NUMBER OF REFLECTIONS : 48594 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) : 0.200 REMARK 3 R VALUE (WORKING SET) : 0.198 REMARK 3 FREE R VALUE : 0.232 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2561 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) : 3479 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.21 REMARK 3 BIN R VALUE (WORKING SET) : 0.4110 REMARK 3 BIN FREE R VALUE SET COUNT : 174 REMARK 3 BIN FREE R VALUE : 0.4630 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3254 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 90 REMARK 3 SOLVENT ATOMS : 269 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 37.01 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 35.21 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.26000 REMARK 3 B22 (A**2) : 0.47000 REMARK 3 B33 (A**2) : 0.79000 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): 0.126 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.124 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.100 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 6.549 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.960 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.944 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3439 ; 0.011 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4686 ; 1.492 ; 2.001 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 444 ; 7.027 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 143 ;37.133 ;24.545 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 560 ;13.906 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 21 ;16.115 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 545 ; 0.121 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2576 ; 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): 1744 ; 1.970 ; 1.833 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2179 ; 2.622 ; 2.734 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1695 ; 3.087 ; 2.147 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): 8.3294 75.8096 -22.2046 REMARK 3 T TENSOR REMARK 3 T11: 0.1224 T22: 0.2707 REMARK 3 T33: 0.0835 T12: 0.0238 REMARK 3 T13: -0.0197 T23: 0.0822 REMARK 3 L TENSOR REMARK 3 L11: 4.3463 L22: 3.3946 REMARK 3 L33: 2.4679 L12: 0.3906 REMARK 3 L13: -1.1674 L23: -1.2157 REMARK 3 S TENSOR REMARK 3 S11: 0.0678 S12: 0.6654 S13: 0.2185 REMARK 3 S21: -0.4239 S22: 0.0447 S23: 0.2256 REMARK 3 S31: 0.0538 S32: -0.3296 S33: -0.1125 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): 1.5161 63.9083 4.4001 REMARK 3 T TENSOR REMARK 3 T11: 0.0095 T22: 0.0094 REMARK 3 T33: 0.0867 T12: -0.0082 REMARK 3 T13: 0.0085 T23: 0.0005 REMARK 3 L TENSOR REMARK 3 L11: 2.0093 L22: 1.4647 REMARK 3 L33: 3.4677 L12: 0.2220 REMARK 3 L13: -0.4416 L23: -0.8216 REMARK 3 S TENSOR REMARK 3 S11: -0.0162 S12: 0.0614 S13: -0.0693 REMARK 3 S21: -0.0149 S22: 0.0278 S23: 0.1239 REMARK 3 S31: 0.1157 S32: -0.1351 S33: -0.0116 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): 7.3997 86.2102 19.9980 REMARK 3 T TENSOR REMARK 3 T11: 0.1017 T22: 0.0517 REMARK 3 T33: 0.0952 T12: -0.0306 REMARK 3 T13: 0.0040 T23: -0.0524 REMARK 3 L TENSOR REMARK 3 L11: 3.1661 L22: 4.0610 REMARK 3 L33: 3.1722 L12: -0.1887 REMARK 3 L13: -0.0190 L23: 1.5912 REMARK 3 S TENSOR REMARK 3 S11: -0.0330 S12: -0.1699 S13: 0.1640 REMARK 3 S21: 0.1141 S22: 0.0356 S23: -0.0625 REMARK 3 S31: -0.0618 S32: -0.0264 S33: -0.0027 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 5A5F 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_1290064091. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-APR-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.4 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID29 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97623 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 51890 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 46.460 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.2 REMARK 200 DATA REDUNDANCY : 5.400 REMARK 200 R MERGE (I) : 0.06000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 23.7500 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) : 2.01 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.8 REMARK 200 DATA REDUNDANCY IN SHELL : 5.50 REMARK 200 R MERGE FOR SHELL (I) : 0.62000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.220 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 (%): 63.55 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.37 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 4 MG/ML PROTEIN, 1 MM UMA, 5 MM AMP REMARK 280 -PNP, 1 MM NAN3, 1 MM DTT, 20 MM HEPES, PH 7.4, 1.8 M NA-MALONATE 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 33.22000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 54.27000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 44.92000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 54.27000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 33.22000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 44.92000 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 GLY A 222 REMARK 465 ALA A 223 REMARK 465 ASP A 224 REMARK 465 GLU A 225 REMARK 465 ARG A 226 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 LEU A 376 CA - CB - CG ANGL. DEV. = -14.4 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 LEU A 13 53.23 -117.26 REMARK 500 GLU A 181 108.14 -49.03 REMARK 500 LEU A 256 138.75 -174.93 REMARK 500 PHE A 303 58.08 33.23 REMARK 500 ARG A 380 81.26 -164.54 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE UMA A 450 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ADP A 451 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MLI A 500 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MLI A 501 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5A5E RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF MURD LIGASE FROM ESCHERICHIA COLI DBREF 5A5F A 1 437 UNP P14900 MURD_ECOLI 2 438 SEQADV 5A5F SER A 438 UNP P14900 EXPRESSION TAG SEQRES 1 A 438 ALA ASP TYR GLN GLY LYS ASN VAL VAL ILE ILE GLY LEU SEQRES 2 A 438 GLY LEU THR GLY LEU SER CYS VAL ASP PHE PHE LEU ALA SEQRES 3 A 438 ARG GLY VAL THR PRO ARG VAL MET ASP THR ARG MET THR SEQRES 4 A 438 PRO PRO GLY LEU ASP LYS LEU PRO GLU ALA VAL GLU ARG SEQRES 5 A 438 HIS THR GLY SER LEU ASN ASP GLU TRP LEU MET ALA ALA SEQRES 6 A 438 ASP LEU ILE VAL ALA SER PRO GLY ILE ALA LEU ALA HIS SEQRES 7 A 438 PRO SER LEU SER ALA ALA ALA ASP ALA GLY ILE GLU ILE SEQRES 8 A 438 VAL GLY ASP ILE GLU LEU PHE CYS ARG GLU ALA GLN ALA SEQRES 9 A 438 PRO ILE VAL ALA ILE THR GLY SER ASN GLY LYS SER THR SEQRES 10 A 438 VAL THR THR LEU VAL GLY GLU MET ALA LYS ALA ALA GLY SEQRES 11 A 438 VAL ASN VAL GLY VAL GLY GLY ASN ILE GLY LEU PRO ALA SEQRES 12 A 438 LEU MET LEU LEU ASP ASP GLU CYS GLU LEU TYR VAL LEU SEQRES 13 A 438 GLU LEU SER SER PHE GLN LEU GLU THR THR SER SER LEU SEQRES 14 A 438 GLN ALA VAL ALA ALA THR ILE LEU ASN VAL THR GLU ASP SEQRES 15 A 438 HIS MET ASP ARG TYR PRO PHE GLY LEU GLN GLN TYR ARG SEQRES 16 A 438 ALA ALA LYS LEU ARG ILE TYR GLU ASN ALA LYS VAL CYS SEQRES 17 A 438 VAL VAL ASN ALA ASP ASP ALA LEU THR MET PRO ILE ARG SEQRES 18 A 438 GLY ALA ASP GLU ARG CYS VAL SER PHE GLY VAL ASN MET SEQRES 19 A 438 GLY ASP TYR HIS LEU ASN HIS GLN GLN GLY GLU THR TRP SEQRES 20 A 438 LEU ARG VAL LYS GLY GLU LYS VAL LEU ASN VAL LYS GLU SEQRES 21 A 438 MET LYS LEU SER GLY GLN HIS ASN TYR THR ASN ALA LEU SEQRES 22 A 438 ALA ALA LEU ALA LEU ALA ASP ALA ALA GLY LEU PRO ARG SEQRES 23 A 438 ALA SER SER LEU LYS ALA LEU THR THR PHE THR GLY LEU SEQRES 24 A 438 PRO HIS ARG PHE GLU VAL VAL LEU GLU HIS ASN GLY VAL SEQRES 25 A 438 ARG TRP ILE ASN ASP SER LYS ALA THR ASN VAL GLY SER SEQRES 26 A 438 THR GLU ALA ALA LEU ASN GLY LEU HIS VAL ASP GLY THR SEQRES 27 A 438 LEU HIS LEU LEU LEU GLY GLY ASP GLY LYS SER ALA ASP SEQRES 28 A 438 PHE SER PRO LEU ALA ARG TYR LEU ASN GLY ASP ASN VAL SEQRES 29 A 438 ARG LEU TYR CYS PHE GLY ARG ASP GLY ALA GLN LEU ALA SEQRES 30 A 438 ALA LEU ARG PRO GLU VAL ALA GLU GLN THR GLU THR MET SEQRES 31 A 438 GLU GLN ALA MET ARG LEU LEU ALA PRO ARG VAL GLN PRO SEQRES 32 A 438 GLY ASP MET VAL LEU LEU SER PRO ALA CYS ALA SER LEU SEQRES 33 A 438 ASP GLN PHE LYS ASN PHE GLU GLN ARG GLY ASN GLU PHE SEQRES 34 A 438 ALA ARG LEU ALA LYS GLU LEU GLY SER HET UMA A 450 49 HET ADP A 451 27 HET MLI A 500 7 HET MLI A 501 7 HETNAM UMA URIDINE-5'-DIPHOSPHATE-N-ACETYLMURAMOYL-L-ALANINE HETNAM ADP ADENOSINE-5'-DIPHOSPHATE HETNAM MLI MALONATE ION FORMUL 2 UMA C23 H36 N4 O20 P2 FORMUL 3 ADP C10 H15 N5 O10 P2 FORMUL 4 MLI 2(C3 H2 O4 2-) FORMUL 6 HOH *269(H2 O) HELIX 1 1 GLY A 14 ARG A 27 1 14 HELIX 2 2 GLY A 42 LEU A 46 5 5 HELIX 3 3 ASN A 58 ALA A 65 1 8 HELIX 4 4 HIS A 78 ALA A 87 1 10 HELIX 5 5 GLY A 93 ALA A 102 1 10 HELIX 6 6 GLY A 114 ALA A 129 1 16 HELIX 7 7 PRO A 142 LEU A 147 5 6 HELIX 8 8 SER A 159 THR A 165 1 7 HELIX 9 9 HIS A 183 TYR A 187 5 5 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 GLY A 332 1 11 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 SER A 438 1 18 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 VAL A 228 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 2.05 SITE 1 AC1 24 GLY A 14 LEU A 15 THR A 16 ASP A 35 SITE 2 AC1 24 THR A 36 ARG A 37 SER A 71 PRO A 72 SITE 3 AC1 24 GLY A 73 GLY A 137 ASN A 138 GLY A 140 SITE 4 AC1 24 SER A 159 GLN A 162 HIS A 183 HOH A2009 SITE 5 AC1 24 HOH A2010 HOH A2012 HOH A2059 HOH A2071 SITE 6 AC1 24 HOH A2095 HOH A2265 HOH A2266 HOH A2267 SITE 1 AC2 22 ASN A 113 GLY A 114 LYS A 115 SER A 116 SITE 2 AC2 22 THR A 117 ASN A 178 HIS A 267 ASN A 271 SITE 3 AC2 22 ARG A 302 PHE A 303 ASP A 317 LYS A 319 SITE 4 AC2 22 ALA A 320 SER A 325 ALA A 328 HOH A2068 SITE 5 AC2 22 HOH A2071 HOH A2072 HOH A2074 HOH A2119 SITE 6 AC2 22 HOH A2184 HOH A2268 SITE 1 AC3 6 THR A 321 ALA A 414 SER A 415 ASN A 421 SITE 2 AC3 6 PHE A 422 HOH A2212 SITE 1 AC4 5 HIS A 241 THR A 246 HIS A 334 HOH A2181 SITE 2 AC4 5 HOH A2269 CRYST1 66.440 89.840 108.540 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 0.015051 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011131 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009213 0.00000