HEADER BIOSYNTHETIC PROTEIN 07-DEC-20 7B6M TITLE CRYSTAL STRUCTURE OF MURE FROM E.COLI IN COMPLEX WITH Z1198948504 COMPND MOL_ID: 1; COMPND 2 MOLECULE: UDP-N-ACETYLMURAMOYL-L-ALANYL-D-GLUTAMATE-2,6- COMPND 3 DIAMINOPIMELATE LIGASE; COMPND 4 CHAIN: A, B; COMPND 5 SYNONYM: MESO-A2PM-ADDING ENZYME,MESO-DIAMINOPIMELATE-ADDING ENZYME, COMPND 6 UDP-MURNAC-L-ALA-D-GLU:MESO-DIAMINOPIMELATE LIGASE,UDP-MURNAC- COMPND 7 TRIPEPTIDE SYNTHETASE,UDP-N-ACETYLMURAMYL-TRIPEPTIDE SYNTHETASE; COMPND 8 EC: 6.3.2.13; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI (STRAIN K12); SOURCE 3 ORGANISM_TAXID: 83333; SOURCE 4 STRAIN: K12; SOURCE 5 GENE: MURE, B0085, JW0083; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: -R3-ROSETTA; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PNIC28-BSA4 KEYWDS UDP-N-ACETYLMURAMOYL-L-ALANYL-D-GLUTAMATE-2, 6-DIAMINOPIMELATE LIGASE KEYWDS 2 CELL WALL BIOSYNTHESIS LIGASE DRUG TARGET, STRUCTURAL GENOMICS, KEYWDS 3 STRUCTURAL GENOMICS CONSORTIUM, SGC, BIOSYNTHETIC PROTEIN, FRAGMENT KEYWDS 4 SCREENING, STRUCTURAL GENOMICS CONSORTIUM FOR RESEARCH ON GENE KEYWDS 5 EXPRESSION, SGCGES EXPDTA X-RAY DIFFRACTION AUTHOR L.KOEKEMOER,M.STEINDEL,M.FAIRHEAD,C.H.ARROWSMITH,A.M.EDWARDS, AUTHOR 2 C.BOUNTRA,F.VON DELFT,T.KROJER,STRUCTURAL GENOMICS CONSORTIUM (SGC), AUTHOR 3 STRUCTURAL GENOMICS CONSORTIUM FOR RESEARCH ON GENE EXPRESSION AUTHOR 4 (SGCGES) REVDAT 2 31-JAN-24 7B6M 1 REMARK REVDAT 1 23-DEC-20 7B6M 0 JRNL AUTH L.KOEKEMOER,M.STEINDEL,M.FAIRHEAD,C.H.ARROWSMITH, JRNL AUTH 2 A.M.EDWARDS,C.BOUNTRA,F.VON DELFT,T.KROJER JRNL TITL CRYSTAL STRUCTURE OF MURE FROM E.COLI JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.67 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0258 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) : 1.67 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 56.13 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 97.0 REMARK 3 NUMBER OF REFLECTIONS : 99570 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) : 0.197 REMARK 3 FREE R VALUE : 0.226 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 5356 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) : 1.67 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.71 REMARK 3 REFLECTION IN BIN (WORKING SET) : 7083 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 92.54 REMARK 3 BIN R VALUE (WORKING SET) : 0.3670 REMARK 3 BIN FREE R VALUE SET COUNT : 320 REMARK 3 BIN FREE R VALUE : 0.3810 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 7282 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 27 REMARK 3 SOLVENT ATOMS : 391 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 34.44 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.24000 REMARK 3 B22 (A**2) : -0.18000 REMARK 3 B33 (A**2) : -0.71000 REMARK 3 B12 (A**2) : 1.07000 REMARK 3 B13 (A**2) : -0.01000 REMARK 3 B23 (A**2) : 0.41000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.114 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.109 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.107 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.523 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.963 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.949 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 7566 ; 0.009 ; 0.018 REMARK 3 BOND LENGTHS OTHERS (A): 7059 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 10290 ; 1.299 ; 1.882 REMARK 3 BOND ANGLES OTHERS (DEGREES): 16297 ; 1.103 ; 2.930 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 986 ; 5.504 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 332 ;32.061 ;23.886 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1220 ;12.377 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 56 ;14.544 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 1170 ; 0.080 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 8700 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1524 ; 0.001 ; 0.020 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): 3922 ; 2.653 ; 3.200 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 3923 ; 2.653 ; 3.200 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4917 ; 3.834 ; 4.785 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 4917 ; 3.834 ; 4.785 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 3644 ; 3.542 ; 3.746 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 3645 ; 3.542 ; 3.747 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 5372 ; 5.496 ; 5.428 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 8215 ; 7.292 ;39.055 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 8150 ; 7.274 ;38.913 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 : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.30 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS REMARK 3 U VALUES : REFINED INDIVIDUALLY REMARK 4 REMARK 4 7B6M COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 08-DEC-20. REMARK 100 THE DEPOSITION ID IS D_1292112742. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-FEB-20 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I03 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.96862 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 S 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XIA2 REMARK 200 DATA SCALING SOFTWARE : XIA2 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 99570 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.670 REMARK 200 RESOLUTION RANGE LOW (A) : 56.130 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.1 REMARK 200 DATA REDUNDANCY : 3.500 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.74 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.83 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL 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: 7B53 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.30 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.25 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M CITRATE PH 5.5 10% PEG4K 19.7% 2 REMARK 280 -PROPANOL, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,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 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: MONOMER REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMER REMARK 350 SOFTWARE USED: PISA AND GEL FILTRATION 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 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMER REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMER REMARK 350 SOFTWARE USED: PISA AND GEL FILTRATION REMARK 350 APPLY THE FOLLOWING TO CHAINS: B 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 SER A 0 REMARK 465 MET A 1 REMARK 465 ALA A 2 REMARK 465 ASP A 3 REMARK 465 THR A 155 REMARK 465 GLU A 156 REMARK 465 ASN A 157 REMARK 465 THR A 158 REMARK 465 THR A 159 REMARK 465 SER B 0 REMARK 465 MET B 1 REMARK 465 ALA B 2 REMARK 465 ASP B 3 REMARK 465 HIS B 44 REMARK 465 GLN B 45 REMARK 465 THR B 155 REMARK 465 GLU B 156 REMARK 465 ASN B 157 REMARK 465 THR B 158 REMARK 465 THR B 159 REMARK 465 ARG B 209 REMARK 465 ASP B 210 REMARK 465 HIS B 211 REMARK 465 LEU B 212 REMARK 465 ASP B 213 REMARK 465 TYR B 214 REMARK 465 HIS B 215 REMARK 465 GLY B 216 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 O HOH B 702 O HOH B 746 1.98 REMARK 500 O HOH B 609 O HOH B 716 2.02 REMARK 500 O LYS B 351 O HOH B 601 2.11 REMARK 500 OE1 GLU A 300 O HOH A 601 2.11 REMARK 500 O GLU B 403 O HOH B 602 2.14 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 NH1 ARG A 335 O ASP B 263 1565 2.09 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 ARG A 23 -87.29 -96.85 REMARK 500 HIS A 44 107.27 -42.12 REMARK 500 GLN A 45 14.86 52.03 REMARK 500 ASP A 69 -3.07 73.77 REMARK 500 ASN A 206 162.27 178.16 REMARK 500 ALA A 359 115.95 -39.37 REMARK 500 ARG A 417 -127.19 56.76 REMARK 500 ARG B 23 -86.34 -96.30 REMARK 500 ASP B 69 -5.22 75.02 REMARK 500 ASN B 206 162.24 179.79 REMARK 500 ARG B 417 -128.11 56.65 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 GLU A 442 GLY A 443 -147.25 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 EDO A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SZN B 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO B 502 DBREF 7B6M A 1 495 UNP P22188 MURE_ECOLI 1 495 DBREF 7B6M B 1 495 UNP P22188 MURE_ECOLI 1 495 SEQADV 7B6M SER A 0 UNP P22188 EXPRESSION TAG SEQADV 7B6M SER B 0 UNP P22188 EXPRESSION TAG SEQRES 1 A 496 SER MET ALA ASP ARG ASN LEU ARG ASP LEU LEU ALA PRO SEQRES 2 A 496 TRP VAL PRO ASP ALA PRO SER ARG ALA LEU ARG GLU MET SEQRES 3 A 496 THR LEU ASP SER ARG VAL ALA ALA ALA GLY ASP LEU PHE SEQRES 4 A 496 VAL ALA VAL VAL GLY HIS GLN ALA ASP GLY ARG ARG TYR SEQRES 5 A 496 ILE PRO GLN ALA ILE ALA GLN GLY VAL ALA ALA ILE ILE SEQRES 6 A 496 ALA GLU ALA LYS ASP GLU ALA THR ASP GLY GLU ILE ARG SEQRES 7 A 496 GLU MET HIS GLY VAL PRO VAL ILE TYR LEU SER GLN LEU SEQRES 8 A 496 ASN GLU ARG LEU SER ALA LEU ALA GLY ARG PHE TYR HIS SEQRES 9 A 496 GLU PRO SER ASP ASN LEU ARG LEU VAL GLY VAL THR GLY SEQRES 10 A 496 THR ASN GLY LYS THR THR THR THR GLN LEU LEU ALA GLN SEQRES 11 A 496 TRP SER GLN LEU LEU GLY GLU ILE SER ALA VAL MET GLY SEQRES 12 A 496 THR VAL GLY ASN GLY LEU LEU GLY LYS VAL ILE PRO THR SEQRES 13 A 496 GLU ASN THR THR GLY SER ALA VAL ASP VAL GLN HIS GLU SEQRES 14 A 496 LEU ALA GLY LEU VAL ASP GLN GLY ALA THR PHE CYS ALA SEQRES 15 A 496 MET GLU VAL SER SER HIS GLY LEU VAL GLN HIS ARG VAL SEQRES 16 A 496 ALA ALA LEU LYS PHE ALA ALA SER VAL PHE THR ASN LEU SEQRES 17 A 496 SER ARG ASP HIS LEU ASP TYR HIS GLY ASP MET GLU HIS SEQRES 18 A 496 TYR GLU ALA ALA LYS TRP LEU LEU TYR SER GLU HIS HIS SEQRES 19 A 496 CYS GLY GLN ALA ILE ILE ASN ALA ASP ASP GLU VAL GLY SEQRES 20 A 496 ARG ARG TRP LEU ALA LYS LEU PRO ASP ALA VAL ALA VAL SEQRES 21 A 496 SER MET GLU ASP HIS ILE ASN PRO ASN CYS HIS GLY ARG SEQRES 22 A 496 TRP LEU LYS ALA THR GLU VAL ASN TYR HIS ASP SER GLY SEQRES 23 A 496 ALA THR ILE ARG PHE SER SER SER TRP GLY ASP GLY GLU SEQRES 24 A 496 ILE GLU SER HIS LEU MET GLY ALA PHE ASN VAL SER ASN SEQRES 25 A 496 LEU LEU LEU ALA LEU ALA THR LEU LEU ALA LEU GLY TYR SEQRES 26 A 496 PRO LEU ALA ASP LEU LEU LYS THR ALA ALA ARG LEU GLN SEQRES 27 A 496 PRO VAL CYS GLY ARG MET GLU VAL PHE THR ALA PRO GLY SEQRES 28 A 496 LYS PRO THR VAL VAL VAL ASP TYR ALA HIS THR PRO ASP SEQRES 29 A 496 ALA LEU GLU LYS ALA LEU GLN ALA ALA ARG LEU HIS CYS SEQRES 30 A 496 ALA GLY LYS LEU TRP CYS VAL PHE GLY CYS GLY GLY ASP SEQRES 31 A 496 ARG ASP LYS GLY LYS ARG PRO LEU MET GLY ALA ILE ALA SEQRES 32 A 496 GLU GLU PHE ALA ASP VAL ALA VAL VAL THR ASP ASP ASN SEQRES 33 A 496 PRO ARG THR GLU GLU PRO ARG ALA ILE ILE ASN ASP ILE SEQRES 34 A 496 LEU ALA GLY MET LEU ASP ALA GLY HIS ALA LYS VAL MET SEQRES 35 A 496 GLU GLY ARG ALA GLU ALA VAL THR CYS ALA VAL MET GLN SEQRES 36 A 496 ALA LYS GLU ASN ASP VAL VAL LEU VAL ALA GLY LYS GLY SEQRES 37 A 496 HIS GLU ASP TYR GLN ILE VAL GLY ASN GLN ARG LEU ASP SEQRES 38 A 496 TYR SER ASP ARG VAL THR VAL ALA ARG LEU LEU GLY VAL SEQRES 39 A 496 ILE ALA SEQRES 1 B 496 SER MET ALA ASP ARG ASN LEU ARG ASP LEU LEU ALA PRO SEQRES 2 B 496 TRP VAL PRO ASP ALA PRO SER ARG ALA LEU ARG GLU MET SEQRES 3 B 496 THR LEU ASP SER ARG VAL ALA ALA ALA GLY ASP LEU PHE SEQRES 4 B 496 VAL ALA VAL VAL GLY HIS GLN ALA ASP GLY ARG ARG TYR SEQRES 5 B 496 ILE PRO GLN ALA ILE ALA GLN GLY VAL ALA ALA ILE ILE SEQRES 6 B 496 ALA GLU ALA LYS ASP GLU ALA THR ASP GLY GLU ILE ARG SEQRES 7 B 496 GLU MET HIS GLY VAL PRO VAL ILE TYR LEU SER GLN LEU SEQRES 8 B 496 ASN GLU ARG LEU SER ALA LEU ALA GLY ARG PHE TYR HIS SEQRES 9 B 496 GLU PRO SER ASP ASN LEU ARG LEU VAL GLY VAL THR GLY SEQRES 10 B 496 THR ASN GLY LYS THR THR THR THR GLN LEU LEU ALA GLN SEQRES 11 B 496 TRP SER GLN LEU LEU GLY GLU ILE SER ALA VAL MET GLY SEQRES 12 B 496 THR VAL GLY ASN GLY LEU LEU GLY LYS VAL ILE PRO THR SEQRES 13 B 496 GLU ASN THR THR GLY SER ALA VAL ASP VAL GLN HIS GLU SEQRES 14 B 496 LEU ALA GLY LEU VAL ASP GLN GLY ALA THR PHE CYS ALA SEQRES 15 B 496 MET GLU VAL SER SER HIS GLY LEU VAL GLN HIS ARG VAL SEQRES 16 B 496 ALA ALA LEU LYS PHE ALA ALA SER VAL PHE THR ASN LEU SEQRES 17 B 496 SER ARG ASP HIS LEU ASP TYR HIS GLY ASP MET GLU HIS SEQRES 18 B 496 TYR GLU ALA ALA LYS TRP LEU LEU TYR SER GLU HIS HIS SEQRES 19 B 496 CYS GLY GLN ALA ILE ILE ASN ALA ASP ASP GLU VAL GLY SEQRES 20 B 496 ARG ARG TRP LEU ALA LYS LEU PRO ASP ALA VAL ALA VAL SEQRES 21 B 496 SER MET GLU ASP HIS ILE ASN PRO ASN CYS HIS GLY ARG SEQRES 22 B 496 TRP LEU LYS ALA THR GLU VAL ASN TYR HIS ASP SER GLY SEQRES 23 B 496 ALA THR ILE ARG PHE SER SER SER TRP GLY ASP GLY GLU SEQRES 24 B 496 ILE GLU SER HIS LEU MET GLY ALA PHE ASN VAL SER ASN SEQRES 25 B 496 LEU LEU LEU ALA LEU ALA THR LEU LEU ALA LEU GLY TYR SEQRES 26 B 496 PRO LEU ALA ASP LEU LEU LYS THR ALA ALA ARG LEU GLN SEQRES 27 B 496 PRO VAL CYS GLY ARG MET GLU VAL PHE THR ALA PRO GLY SEQRES 28 B 496 LYS PRO THR VAL VAL VAL ASP TYR ALA HIS THR PRO ASP SEQRES 29 B 496 ALA LEU GLU LYS ALA LEU GLN ALA ALA ARG LEU HIS CYS SEQRES 30 B 496 ALA GLY LYS LEU TRP CYS VAL PHE GLY CYS GLY GLY ASP SEQRES 31 B 496 ARG ASP LYS GLY LYS ARG PRO LEU MET GLY ALA ILE ALA SEQRES 32 B 496 GLU GLU PHE ALA ASP VAL ALA VAL VAL THR ASP ASP ASN SEQRES 33 B 496 PRO ARG THR GLU GLU PRO ARG ALA ILE ILE ASN ASP ILE SEQRES 34 B 496 LEU ALA GLY MET LEU ASP ALA GLY HIS ALA LYS VAL MET SEQRES 35 B 496 GLU GLY ARG ALA GLU ALA VAL THR CYS ALA VAL MET GLN SEQRES 36 B 496 ALA LYS GLU ASN ASP VAL VAL LEU VAL ALA GLY LYS GLY SEQRES 37 B 496 HIS GLU ASP TYR GLN ILE VAL GLY ASN GLN ARG LEU ASP SEQRES 38 B 496 TYR SER ASP ARG VAL THR VAL ALA ARG LEU LEU GLY VAL SEQRES 39 B 496 ILE ALA HET EDO A 501 4 HET SZN B 501 19 HET EDO B 502 4 HETNAM EDO 1,2-ETHANEDIOL HETNAM SZN N-[2-(2,5-DIOXOPYRROLIDIN-1-YL)ETHYL]-3-METHYLBENZAMIDE HETSYN EDO ETHYLENE GLYCOL HETSYN SZN ~{N}-[2-[2,5-BIS(OXIDANYLIDENE)PYRROLIDIN-1-YL]ETHYL]- HETSYN 2 SZN 3-METHYL-BENZAMIDE FORMUL 3 EDO 2(C2 H6 O2) FORMUL 4 SZN C14 H16 N2 O3 FORMUL 6 HOH *391(H2 O) HELIX 1 AA1 ASN A 5 ALA A 11 1 7 HELIX 2 AA2 TYR A 51 GLN A 58 1 8 HELIX 3 AA3 GLN A 89 TYR A 102 1 14 HELIX 4 AA4 GLU A 104 ASN A 108 5 5 HELIX 5 AA5 GLY A 119 LEU A 134 1 16 HELIX 6 AA6 SER A 161 GLN A 175 1 15 HELIX 7 AA7 SER A 185 GLN A 191 1 7 HELIX 8 AA8 TYR A 214 HIS A 232 1 19 HELIX 9 AA9 ASP A 243 LEU A 253 1 11 HELIX 10 AB1 ASN A 266 HIS A 270 5 5 HELIX 11 AB2 GLY A 305 LEU A 322 1 18 HELIX 12 AB3 PRO A 325 ALA A 333 1 9 HELIX 13 AB4 ALA A 334 LEU A 336 5 3 HELIX 14 AB5 THR A 361 HIS A 375 1 15 HELIX 15 AB6 GLY A 393 ALA A 406 1 14 HELIX 16 AB7 GLU A 420 GLY A 431 1 12 HELIX 17 AB8 ASP A 434 ALA A 438 5 5 HELIX 18 AB9 GLY A 443 ALA A 455 1 13 HELIX 19 AC1 SER A 482 GLY A 492 1 11 HELIX 20 AC2 ASN B 5 ALA B 11 1 7 HELIX 21 AC3 ASP B 47 ARG B 50 5 4 HELIX 22 AC4 TYR B 51 GLN B 58 1 8 HELIX 23 AC5 GLN B 89 TYR B 102 1 14 HELIX 24 AC6 GLU B 104 ASN B 108 5 5 HELIX 25 AC7 GLY B 119 LEU B 134 1 16 HELIX 26 AC8 SER B 161 GLN B 175 1 15 HELIX 27 AC9 SER B 185 GLN B 191 1 7 HELIX 28 AD1 MET B 218 HIS B 232 1 15 HELIX 29 AD2 ASP B 243 LEU B 253 1 11 HELIX 30 AD3 ASN B 266 HIS B 270 5 5 HELIX 31 AD4 GLY B 305 GLY B 323 1 19 HELIX 32 AD5 PRO B 325 ALA B 333 1 9 HELIX 33 AD6 ALA B 334 LEU B 336 5 3 HELIX 34 AD7 THR B 361 HIS B 375 1 15 HELIX 35 AD8 GLY B 393 ALA B 406 1 14 HELIX 36 AD9 GLU B 420 ALA B 430 1 11 HELIX 37 AE1 ASP B 434 ALA B 438 5 5 HELIX 38 AE2 GLY B 443 ALA B 455 1 13 HELIX 39 AE3 SER B 482 GLY B 492 1 11 SHEET 1 AA1 5 MET A 25 THR A 26 0 SHEET 2 AA1 5 LEU A 37 ALA A 40 1 O VAL A 39 N THR A 26 SHEET 3 AA1 5 ALA A 62 GLU A 66 1 O ILE A 64 N ALA A 40 SHEET 4 AA1 5 VAL A 82 LEU A 87 1 O ILE A 85 N ILE A 63 SHEET 5 AA1 5 ILE A 76 MET A 79 -1 N ARG A 77 O VAL A 84 SHEET 1 AA2 2 VAL A 42 GLY A 43 0 SHEET 2 AA2 2 ALA A 46 ASP A 47 -1 O ALA A 46 N GLY A 43 SHEET 1 AA310 GLY A 145 LEU A 148 0 SHEET 2 AA310 SER A 138 GLY A 142 -1 N VAL A 140 O GLY A 147 SHEET 3 AA310 PHE A 179 GLU A 183 1 O GLU A 183 N MET A 141 SHEET 4 AA310 ARG A 110 THR A 115 1 N VAL A 112 O MET A 182 SHEET 5 AA310 ALA A 201 PHE A 204 1 O VAL A 203 N THR A 115 SHEET 6 AA310 GLN A 236 ASN A 240 1 O GLN A 236 N SER A 202 SHEET 7 AA310 VAL A 257 SER A 260 1 O VAL A 257 N ALA A 237 SHEET 8 AA310 ARG A 272 HIS A 282 1 O ARG A 272 N ALA A 258 SHEET 9 AA310 GLY A 285 SER A 292 -1 O ARG A 289 N GLU A 278 SHEET 10 AA310 GLY A 297 SER A 301 -1 O ILE A 299 N ILE A 288 SHEET 1 AA4 6 GLU A 344 PHE A 346 0 SHEET 2 AA4 6 THR A 353 ASP A 357 -1 O VAL A 354 N PHE A 346 SHEET 3 AA4 6 VAL A 460 ALA A 464 1 O VAL A 463 N VAL A 355 SHEET 4 AA4 6 LEU A 380 PHE A 384 1 N VAL A 383 O LEU A 462 SHEET 5 AA4 6 VAL A 408 VAL A 411 1 O VAL A 410 N CYS A 382 SHEET 6 AA4 6 LYS A 439 VAL A 440 1 O LYS A 439 N ALA A 409 SHEET 1 AA5 2 TYR A 471 VAL A 474 0 SHEET 2 AA5 2 GLN A 477 ASP A 480 -1 O LEU A 479 N GLN A 472 SHEET 1 AA6 5 MET B 25 THR B 26 0 SHEET 2 AA6 5 LEU B 37 ALA B 40 1 O VAL B 39 N THR B 26 SHEET 3 AA6 5 ALA B 62 GLU B 66 1 O ILE B 64 N ALA B 40 SHEET 4 AA6 5 VAL B 82 LEU B 87 1 O ILE B 85 N ILE B 63 SHEET 5 AA6 5 ILE B 76 MET B 79 -1 N ARG B 77 O VAL B 84 SHEET 1 AA710 GLY B 145 LEU B 148 0 SHEET 2 AA710 SER B 138 GLY B 142 -1 N VAL B 140 O GLY B 147 SHEET 3 AA710 PHE B 179 GLU B 183 1 O GLU B 183 N MET B 141 SHEET 4 AA710 ARG B 110 THR B 115 1 N VAL B 112 O MET B 182 SHEET 5 AA710 ALA B 201 PHE B 204 1 O VAL B 203 N THR B 115 SHEET 6 AA710 GLN B 236 ASN B 240 1 O ILE B 238 N SER B 202 SHEET 7 AA710 VAL B 257 SER B 260 1 O VAL B 257 N ALA B 237 SHEET 8 AA710 ARG B 272 HIS B 282 1 O ALA B 276 N SER B 260 SHEET 9 AA710 GLY B 285 SER B 292 -1 O ARG B 289 N GLU B 278 SHEET 10 AA710 GLY B 297 SER B 301 -1 O ILE B 299 N ILE B 288 SHEET 1 AA8 6 GLU B 344 PHE B 346 0 SHEET 2 AA8 6 THR B 353 ASP B 357 -1 O VAL B 354 N PHE B 346 SHEET 3 AA8 6 VAL B 460 ALA B 464 1 O VAL B 463 N VAL B 355 SHEET 4 AA8 6 LEU B 380 PHE B 384 1 N VAL B 383 O LEU B 462 SHEET 5 AA8 6 VAL B 408 VAL B 411 1 O VAL B 410 N CYS B 382 SHEET 6 AA8 6 LYS B 439 VAL B 440 1 O LYS B 439 N ALA B 409 SHEET 1 AA9 2 TYR B 471 VAL B 474 0 SHEET 2 AA9 2 GLN B 477 ASP B 480 -1 O LEU B 479 N GLN B 472 SITE 1 AC1 4 THR A 117 ASN A 118 GLY A 119 LYS A 120 SITE 1 AC2 9 GLY B 113 THR B 115 LEU B 189 PHE B 199 SITE 2 AC2 9 SER B 202 PHE B 204 CYS B 234 VAL B 245 SITE 3 AC2 9 TRP B 249 SITE 1 AC3 7 GLY B 378 LYS B 379 LYS B 456 ASN B 458 SITE 2 AC3 7 ASP B 459 HOH B 708 HOH B 732 CRYST1 58.137 58.153 74.348 97.08 91.49 104.93 P 1 2 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 0.017201 0.004588 0.001073 0.00000 SCALE2 0.000000 0.017797 0.002415 0.00000 SCALE3 0.000000 0.000000 0.013578 0.00000