HEADER BIOSYNTHETIC PROTEIN 07-DEC-20 7B6J TITLE CRYSTAL STRUCTURE OF MURE FROM E.COLI IN COMPLEX WITH MINIFRAG TITLE 2 SUCCINIMIDE 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 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) REVDAT 2 31-JAN-24 7B6J 1 REMARK REVDAT 1 23-DEC-20 7B6J 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. 2.09 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0267 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.09 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.61 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 68208 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : FREE R-VALUE REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.183 REMARK 3 FREE R VALUE : 0.236 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.125 REMARK 3 FREE R VALUE TEST SET COUNT : 3496 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.95 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.00 REMARK 3 REFLECTION IN BIN (WORKING SET) : 4589 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 95.74 REMARK 3 BIN R VALUE (WORKING SET) : 0.3020 REMARK 3 BIN FREE R VALUE SET COUNT : 262 REMARK 3 BIN FREE R VALUE : 0.3170 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 : 37 REMARK 3 SOLVENT ATOMS : 320 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 41.53 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.15900 REMARK 3 B22 (A**2) : 0.72100 REMARK 3 B33 (A**2) : -2.20800 REMARK 3 B12 (A**2) : 2.35400 REMARK 3 B13 (A**2) : 0.50200 REMARK 3 B23 (A**2) : 0.99400 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.174 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.162 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.137 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.087 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.964 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.939 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 7575 ; 0.008 ; 0.013 REMARK 3 BOND LENGTHS OTHERS (A): 7204 ; 0.001 ; 0.017 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 10302 ; 1.487 ; 1.632 REMARK 3 BOND ANGLES OTHERS (DEGREES): 16529 ; 1.331 ; 1.582 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 987 ; 6.831 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 389 ;30.682 ;21.902 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1218 ;13.866 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 56 ;15.557 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 978 ; 0.068 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 8822 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1706 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1388 ; 0.205 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 94 ; 0.205 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 3610 ; 0.152 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 328 ; 0.194 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): 2 ; 0.013 ; 0.200 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): 3929 ; 3.059 ; 4.158 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 3926 ; 3.056 ; 4.157 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4922 ; 4.220 ; 6.216 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 4922 ; 4.220 ; 6.216 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 3646 ; 3.952 ; 4.690 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 3647 ; 3.951 ; 4.690 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 5378 ; 5.936 ; 6.849 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 5379 ; 5.936 ; 6.849 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 : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK BULK SOLVENT 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 THEIR REMARK 3 RIDING POSITIONS REMARK 4 REMARK 4 7B6J 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_1292112739. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-OCT-19 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) : 0.97625 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 : 68240 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.950 REMARK 200 RESOLUTION RANGE LOW (A) : 47.610 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 6.600 REMARK 200 R MERGE (I) : 0.10000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.95 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.7 REMARK 200 DATA REDUNDANCY IN SHELL : 3.60 REMARK 200 R MERGE FOR SHELL (I) : 0.82300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.200 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 (%): 45.78 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.27 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M CITRATE PH 5.5 11.6% PEG4K 18.4% REMARK 280 2-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 669 O HOH B 755 1.89 REMARK 500 O HOH B 676 O HOH B 747 2.01 REMARK 500 O HOH B 608 O HOH B 617 2.12 REMARK 500 O HOH A 747 O HOH A 750 2.18 REMARK 500 O HOH B 739 O HOH B 750 2.19 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 OE2 GLU A 420 NH2 ARG B 422 1464 1.96 REMARK 500 O HOH A 608 O HOH B 728 1464 2.06 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 -92.06 -92.52 REMARK 500 LYS A 68 109.40 -45.24 REMARK 500 SER A 208 50.43 -106.92 REMARK 500 HIS A 211 1.39 81.23 REMARK 500 ARG A 417 -124.74 57.74 REMARK 500 GLU A 420 108.10 -53.15 REMARK 500 ASP A 470 43.60 -77.45 REMARK 500 ARG B 23 -91.38 -93.97 REMARK 500 LYS B 68 122.52 -38.83 REMARK 500 GLU B 70 -43.80 -137.65 REMARK 500 MET B 218 -51.91 56.04 REMARK 500 PRO B 349 122.42 -37.05 REMARK 500 ARG B 417 -124.75 55.42 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 -127.47 REMARK 500 GLU B 442 GLY B 443 -131.62 REMARK 500 REMARK 500 REMARK: NULL DBREF 7B6J A 1 495 UNP P22188 MURE_ECOLI 1 495 DBREF 7B6J B 1 495 UNP P22188 MURE_ECOLI 1 495 SEQADV 7B6J SER A 0 UNP P22188 EXPRESSION TAG SEQADV 7B6J 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 SZB A 502 7 HET SZB A 503 7 HET IPA A 504 4 HET EDO B 501 4 HET SZB B 502 7 HET IPA B 503 4 HETNAM EDO 1,2-ETHANEDIOL HETNAM SZB SUCCINIMIDE HETNAM IPA ISOPROPYL ALCOHOL HETSYN EDO ETHYLENE GLYCOL HETSYN SZB PYRROLIDINE-2,5-DIONE; PYRROLE-2,5-DIONE; 2,5- HETSYN 2 SZB PYRROLIDINEDIONE HETSYN IPA 2-PROPANOL FORMUL 3 EDO 2(C2 H6 O2) FORMUL 4 SZB 3(C4 H3 N O2) FORMUL 6 IPA 2(C3 H8 O) FORMUL 10 HOH *320(H2 O) HELIX 1 AA1 ASN A 5 ALA A 11 1 7 HELIX 2 AA2 ASP A 47 ARG A 50 5 4 HELIX 3 AA3 TYR A 51 GLN A 58 1 8 HELIX 4 AA4 GLN A 89 TYR A 102 1 14 HELIX 5 AA5 GLU A 104 ASN A 108 5 5 HELIX 6 AA6 GLY A 119 LEU A 134 1 16 HELIX 7 AA7 SER A 161 GLN A 175 1 15 HELIX 8 AA8 SER A 185 GLN A 191 1 7 HELIX 9 AA9 TYR A 214 HIS A 232 1 19 HELIX 10 AB1 ASP A 243 ALA A 251 1 9 HELIX 11 AB2 ASN A 266 HIS A 270 5 5 HELIX 12 AB3 GLY A 305 LEU A 322 1 18 HELIX 13 AB4 PRO A 325 ALA A 333 1 9 HELIX 14 AB5 ALA A 334 LEU A 336 5 3 HELIX 15 AB6 THR A 361 HIS A 375 1 15 HELIX 16 AB7 GLY A 393 ALA A 406 1 14 HELIX 17 AB8 GLU A 420 GLY A 431 1 12 HELIX 18 AB9 ASP A 434 ALA A 438 5 5 HELIX 19 AC1 GLY A 443 ALA A 455 1 13 HELIX 20 AC2 SER A 482 GLY A 492 1 11 HELIX 21 AC3 ASN B 5 ALA B 11 1 7 HELIX 22 AC4 ASP B 28 ALA B 32 5 5 HELIX 23 AC5 ASP B 47 ARG B 50 5 4 HELIX 24 AC6 TYR B 51 GLN B 58 1 8 HELIX 25 AC7 GLN B 89 TYR B 102 1 14 HELIX 26 AC8 GLU B 104 ASN B 108 5 5 HELIX 27 AC9 GLY B 119 LEU B 134 1 16 HELIX 28 AD1 SER B 161 GLN B 175 1 15 HELIX 29 AD2 SER B 185 GLN B 191 1 7 HELIX 30 AD3 MET B 218 HIS B 232 1 15 HELIX 31 AD4 ASP B 243 ALA B 251 1 9 HELIX 32 AD5 ASN B 266 HIS B 270 5 5 HELIX 33 AD6 GLY B 305 LEU B 322 1 18 HELIX 34 AD7 PRO B 325 ALA B 333 1 9 HELIX 35 AD8 ALA B 334 LEU B 336 5 3 HELIX 36 AD9 THR B 361 LEU B 374 1 14 HELIX 37 AE1 LYS B 394 ALA B 406 1 13 HELIX 38 AE2 GLU B 420 ALA B 430 1 11 HELIX 39 AE3 ASP B 434 ALA B 438 5 5 HELIX 40 AE4 GLY B 443 ALA B 455 1 13 HELIX 41 AE5 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 LEU A 37 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 AA210 GLY A 145 LEU A 148 0 SHEET 2 AA210 SER A 138 GLY A 142 -1 N VAL A 140 O GLY A 147 SHEET 3 AA210 PHE A 179 GLU A 183 1 O GLU A 183 N MET A 141 SHEET 4 AA210 ARG A 110 THR A 115 1 N VAL A 112 O CYS A 180 SHEET 5 AA210 PHE A 199 PHE A 204 1 O VAL A 203 N THR A 115 SHEET 6 AA210 GLN A 236 ASN A 240 1 O ILE A 238 N SER A 202 SHEET 7 AA210 VAL A 257 SER A 260 1 O VAL A 257 N ILE A 239 SHEET 8 AA210 ARG A 272 HIS A 282 1 O ALA A 276 N SER A 260 SHEET 9 AA210 GLY A 285 SER A 292 -1 O ARG A 289 N GLU A 278 SHEET 10 AA210 GLY A 297 SER A 301 -1 O ILE A 299 N ILE A 288 SHEET 1 AA3 6 GLU A 344 PHE A 346 0 SHEET 2 AA3 6 THR A 353 ASP A 357 -1 O VAL A 354 N PHE A 346 SHEET 3 AA3 6 VAL A 460 ALA A 464 1 O VAL A 463 N VAL A 355 SHEET 4 AA3 6 LEU A 380 PHE A 384 1 N TRP A 381 O LEU A 462 SHEET 5 AA3 6 VAL A 408 VAL A 411 1 O VAL A 408 N CYS A 382 SHEET 6 AA3 6 LYS A 439 VAL A 440 1 O LYS A 439 N ALA A 409 SHEET 1 AA4 2 TYR A 471 VAL A 474 0 SHEET 2 AA4 2 GLN A 477 ASP A 480 -1 O LEU A 479 N GLN A 472 SHEET 1 AA5 5 MET B 25 THR B 26 0 SHEET 2 AA5 5 LEU B 37 ALA B 40 1 O VAL B 39 N THR B 26 SHEET 3 AA5 5 ALA B 62 GLU B 66 1 O ILE B 64 N ALA B 40 SHEET 4 AA5 5 VAL B 82 LEU B 87 1 O ILE B 85 N ILE B 63 SHEET 5 AA5 5 GLU B 75 MET B 79 -1 N ARG B 77 O VAL B 84 SHEET 1 AA610 GLY B 145 LEU B 148 0 SHEET 2 AA610 SER B 138 GLY B 142 -1 N VAL B 140 O GLY B 147 SHEET 3 AA610 PHE B 179 GLU B 183 1 O GLU B 183 N MET B 141 SHEET 4 AA610 ARG B 110 THR B 115 1 N VAL B 112 O CYS B 180 SHEET 5 AA610 ALA B 201 PHE B 204 1 O VAL B 203 N THR B 115 SHEET 6 AA610 GLN B 236 ASN B 240 1 O GLN B 236 N SER B 202 SHEET 7 AA610 VAL B 257 SER B 260 1 O VAL B 257 N ALA B 237 SHEET 8 AA610 ARG B 272 HIS B 282 1 O ALA B 276 N SER B 260 SHEET 9 AA610 GLY B 285 SER B 292 -1 O GLY B 285 N HIS B 282 SHEET 10 AA610 GLY B 297 SER B 301 -1 O ILE B 299 N ILE B 288 SHEET 1 AA7 6 GLU B 344 PHE B 346 0 SHEET 2 AA7 6 THR B 353 ASP B 357 -1 O VAL B 354 N PHE B 346 SHEET 3 AA7 6 VAL B 460 ALA B 464 1 O VAL B 463 N VAL B 355 SHEET 4 AA7 6 LEU B 380 PHE B 384 1 N VAL B 383 O LEU B 462 SHEET 5 AA7 6 VAL B 408 VAL B 411 1 O VAL B 410 N CYS B 382 SHEET 6 AA7 6 LYS B 439 VAL B 440 1 O LYS B 439 N ALA B 409 SHEET 1 AA8 2 TYR B 471 VAL B 474 0 SHEET 2 AA8 2 GLN B 477 ASP B 480 -1 O LEU B 479 N GLN B 472 CRYST1 58.258 58.291 74.633 96.82 91.36 104.99 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 0.017165 0.004597 0.001011 0.00000 SCALE2 0.000000 0.017760 0.002318 0.00000 SCALE3 0.000000 0.000000 0.013516 0.00000