HEADER TRANSFERASE 29-SEP-20 7AJZ TITLE THE X-RAY STRUCTURE OF L,D-TRANSPEPTIDASE LDTA FROM VIBRIO CHOLERAE IN TITLE 2 COMPLEX WITH NAG-NAM(TETRAPEPTIDE) COMPND MOL_ID: 1; COMPND 2 MOLECULE: L,D-TRANSPEPTIDASE YCBB; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: NAG-NAM(TETRAPEPTIDE); COMPND 7 CHAIN: C; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: VIBRIO CHOLERAE; SOURCE 3 ORGANISM_TAXID: 666; SOURCE 4 GENE: ERS013138_01558, ERS013186_00077, ERS013206_00149; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 MOL_ID: 2; SOURCE 8 SYNTHETIC: YES; SOURCE 9 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 10 ORGANISM_TAXID: 32630 KEYWDS L, D-TRANSPEPTIDASE, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR M.T.BATUECAS,J.A.HERMOSO REVDAT 4 31-JAN-24 7AJZ 1 REMARK REVDAT 3 15-NOV-23 7AJZ 1 LINK ATOM REVDAT 2 21-DEC-22 7AJZ 1 COMPND SOURCE REMARK DBREF REVDAT 2 2 1 SEQRES LINK ATOM REVDAT 1 06-OCT-21 7AJZ 0 JRNL AUTH M.T.BATUECAS,J.A.HERMOSO JRNL TITL THE X-RAY STRUCTURE OF L,D-TRANSPEPTIDASE LDTA FROM VIBRIO JRNL TITL 2 CHOLERAE IN COMPLEX WITH NAG-NAM(TETRAPEPTIDE) JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.98 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 : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.98 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.90 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 29567 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) : 0.212 REMARK 3 R VALUE (WORKING SET) : 0.210 REMARK 3 FREE R VALUE : 0.266 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 1537 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) : 2.98 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.06 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2142 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.4040 REMARK 3 BIN FREE R VALUE SET COUNT : 117 REMARK 3 BIN FREE R VALUE : 0.4600 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 7921 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 28 REMARK 3 SOLVENT ATOMS : 24 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 114.3 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.36000 REMARK 3 B22 (A**2) : -1.18000 REMARK 3 B33 (A**2) : 0.82000 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): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.419 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.448 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 27.900 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.956 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.936 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 8157 ; 0.006 ; 0.013 REMARK 3 BOND LENGTHS OTHERS (A): 7593 ; 0.001 ; 0.017 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 11120 ; 1.367 ; 1.641 REMARK 3 BOND ANGLES OTHERS (DEGREES): 17461 ; 1.181 ; 1.582 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 975 ; 6.815 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 456 ;33.927 ;23.092 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1341 ;16.193 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 47 ;14.702 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 1060 ; 0.056 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 9279 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1909 ; 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL 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 NCS TYPE: LOCAL REMARK 3 NUMBER OF DIFFERENT NCS PAIRS : 1 REMARK 3 GROUP CHAIN1 RANGE CHAIN2 RANGE COUNT RMS WEIGHT REMARK 3 1 A 29 511 B 29 511 15014 0.130 0.050 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 : 1.20 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 U VALUES : REFINED INDIVIDUALLY REMARK 4 REMARK 4 7AJZ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 30-SEP-20. REMARK 100 THE DEPOSITION ID IS D_1292111516. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-JUN-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALBA REMARK 200 BEAMLINE : XALOC REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979080 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 31171 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.980 REMARK 200 RESOLUTION RANGE LOW (A) : 48.900 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 10.90 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.98 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.14 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 11.50 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 11.50 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: 7AJ9 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 62.56 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.29 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M HEPES PH 7 + 10% PEG 8000 + 10% REMARK 280 ETHYLENE GLYCOL, VAPOR DIFFUSION, TEMPERATURE 298K 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 28.75500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 138.03200 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 46.27900 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 138.03200 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 28.75500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 46.27900 REMARK 290 SMTRY3 4 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, C 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: MONOMERIC 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 ALA A 17 REMARK 465 ALA A 18 REMARK 465 MET A 19 REMARK 465 VAL A 20 REMARK 465 THR A 21 REMARK 465 GLN A 22 REMARK 465 ARG A 23 REMARK 465 PHE A 24 REMARK 465 VAL A 25 REMARK 465 GLU A 26 REMARK 465 LEU A 27 REMARK 465 GLY A 28 REMARK 465 ASN A 513 REMARK 465 GLY A 514 REMARK 465 ASP A 515 REMARK 465 ALA A 516 REMARK 465 SER A 517 REMARK 465 PRO A 518 REMARK 465 ASN A 519 REMARK 465 LEU A 520 REMARK 465 THR A 521 REMARK 465 LYS A 522 REMARK 465 ILE A 523 REMARK 465 GLU A 524 REMARK 465 ASN A 525 REMARK 465 LEU A 526 REMARK 465 TYR A 527 REMARK 465 PHE A 528 REMARK 465 GLN A 529 REMARK 465 GLY A 530 REMARK 465 SER A 531 REMARK 465 SER A 532 REMARK 465 SER A 533 REMARK 465 HIS A 534 REMARK 465 HIS A 535 REMARK 465 HIS A 536 REMARK 465 HIS A 537 REMARK 465 HIS A 538 REMARK 465 HIS A 539 REMARK 465 ALA B 17 REMARK 465 ALA B 18 REMARK 465 MET B 19 REMARK 465 VAL B 20 REMARK 465 THR B 21 REMARK 465 GLN B 22 REMARK 465 GLY B 514 REMARK 465 ASP B 515 REMARK 465 ALA B 516 REMARK 465 SER B 517 REMARK 465 PRO B 518 REMARK 465 ASN B 519 REMARK 465 LEU B 520 REMARK 465 THR B 521 REMARK 465 LYS B 522 REMARK 465 ILE B 523 REMARK 465 GLU B 524 REMARK 465 ASN B 525 REMARK 465 LEU B 526 REMARK 465 TYR B 527 REMARK 465 PHE B 528 REMARK 465 GLN B 529 REMARK 465 GLY B 530 REMARK 465 SER B 531 REMARK 465 SER B 532 REMARK 465 SER B 533 REMARK 465 HIS B 534 REMARK 465 HIS B 535 REMARK 465 HIS B 536 REMARK 465 HIS B 537 REMARK 465 HIS B 538 REMARK 465 HIS B 539 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 ASN A 54 30.39 77.51 REMARK 500 ARG A 99 49.82 -89.73 REMARK 500 PHE A 130 -56.38 -132.09 REMARK 500 PHE A 187 -1.96 79.54 REMARK 500 HIS A 208 49.52 -153.62 REMARK 500 ASP A 222 99.39 -69.46 REMARK 500 ASP A 229 69.57 -104.87 REMARK 500 ARG A 358 -64.92 -101.65 REMARK 500 ASP A 376 72.07 32.71 REMARK 500 ASP A 386 96.20 -69.91 REMARK 500 ARG A 438 53.76 -110.77 REMARK 500 ASN A 449 46.42 -95.82 REMARK 500 GLU A 494 54.99 38.11 REMARK 500 LEU A 509 -54.27 75.28 REMARK 500 ASN B 54 33.68 75.83 REMARK 500 ARG B 99 49.42 -92.15 REMARK 500 LYS B 123 -62.35 -97.15 REMARK 500 PHE B 130 -57.02 -130.39 REMARK 500 PHE B 187 -6.34 79.22 REMARK 500 HIS B 208 45.64 -154.20 REMARK 500 ASP B 222 99.14 -68.40 REMARK 500 ASN B 228 -70.47 -89.67 REMARK 500 ASP B 229 70.49 -106.38 REMARK 500 ALA B 231 27.45 -142.54 REMARK 500 THR B 252 46.80 -89.58 REMARK 500 SER B 291 103.32 -161.08 REMARK 500 ARG B 358 -66.92 -101.93 REMARK 500 ARG B 438 54.70 -109.31 REMARK 500 ASN B 449 42.97 -92.24 REMARK 500 GLU B 494 51.05 39.32 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 7AJ9 RELATED DB: PDB REMARK 900 7AJ9 CONTAINS THE APO STRUCTURE DBREF1 7AJZ A 22 523 UNP A0A655UKB5_VIBCL DBREF2 7AJZ A A0A655UKB5 22 523 DBREF1 7AJZ B 22 523 UNP A0A655UKB5_VIBCL DBREF2 7AJZ B A0A655UKB5 22 523 DBREF 7AJZ C 2 5 PDB 7AJZ 7AJZ 2 5 SEQADV 7AJZ ALA A 17 UNP A0A655UKB EXPRESSION TAG SEQADV 7AJZ ALA A 18 UNP A0A655UKB EXPRESSION TAG SEQADV 7AJZ MET A 19 UNP A0A655UKB EXPRESSION TAG SEQADV 7AJZ VAL A 20 UNP A0A655UKB EXPRESSION TAG SEQADV 7AJZ THR A 21 UNP A0A655UKB EXPRESSION TAG SEQADV 7AJZ GLU A 524 UNP A0A655UKB EXPRESSION TAG SEQADV 7AJZ ASN A 525 UNP A0A655UKB EXPRESSION TAG SEQADV 7AJZ LEU A 526 UNP A0A655UKB EXPRESSION TAG SEQADV 7AJZ TYR A 527 UNP A0A655UKB EXPRESSION TAG SEQADV 7AJZ PHE A 528 UNP A0A655UKB EXPRESSION TAG SEQADV 7AJZ GLN A 529 UNP A0A655UKB EXPRESSION TAG SEQADV 7AJZ GLY A 530 UNP A0A655UKB EXPRESSION TAG SEQADV 7AJZ SER A 531 UNP A0A655UKB EXPRESSION TAG SEQADV 7AJZ SER A 532 UNP A0A655UKB EXPRESSION TAG SEQADV 7AJZ SER A 533 UNP A0A655UKB EXPRESSION TAG SEQADV 7AJZ HIS A 534 UNP A0A655UKB EXPRESSION TAG SEQADV 7AJZ HIS A 535 UNP A0A655UKB EXPRESSION TAG SEQADV 7AJZ HIS A 536 UNP A0A655UKB EXPRESSION TAG SEQADV 7AJZ HIS A 537 UNP A0A655UKB EXPRESSION TAG SEQADV 7AJZ HIS A 538 UNP A0A655UKB EXPRESSION TAG SEQADV 7AJZ HIS A 539 UNP A0A655UKB EXPRESSION TAG SEQADV 7AJZ ALA B 17 UNP A0A655UKB EXPRESSION TAG SEQADV 7AJZ ALA B 18 UNP A0A655UKB EXPRESSION TAG SEQADV 7AJZ MET B 19 UNP A0A655UKB EXPRESSION TAG SEQADV 7AJZ VAL B 20 UNP A0A655UKB EXPRESSION TAG SEQADV 7AJZ THR B 21 UNP A0A655UKB EXPRESSION TAG SEQADV 7AJZ GLU B 524 UNP A0A655UKB EXPRESSION TAG SEQADV 7AJZ ASN B 525 UNP A0A655UKB EXPRESSION TAG SEQADV 7AJZ LEU B 526 UNP A0A655UKB EXPRESSION TAG SEQADV 7AJZ TYR B 527 UNP A0A655UKB EXPRESSION TAG SEQADV 7AJZ PHE B 528 UNP A0A655UKB EXPRESSION TAG SEQADV 7AJZ GLN B 529 UNP A0A655UKB EXPRESSION TAG SEQADV 7AJZ GLY B 530 UNP A0A655UKB EXPRESSION TAG SEQADV 7AJZ SER B 531 UNP A0A655UKB EXPRESSION TAG SEQADV 7AJZ SER B 532 UNP A0A655UKB EXPRESSION TAG SEQADV 7AJZ SER B 533 UNP A0A655UKB EXPRESSION TAG SEQADV 7AJZ HIS B 534 UNP A0A655UKB EXPRESSION TAG SEQADV 7AJZ HIS B 535 UNP A0A655UKB EXPRESSION TAG SEQADV 7AJZ HIS B 536 UNP A0A655UKB EXPRESSION TAG SEQADV 7AJZ HIS B 537 UNP A0A655UKB EXPRESSION TAG SEQADV 7AJZ HIS B 538 UNP A0A655UKB EXPRESSION TAG SEQADV 7AJZ HIS B 539 UNP A0A655UKB EXPRESSION TAG SEQRES 1 A 523 ALA ALA MET VAL THR GLN ARG PHE VAL GLU LEU GLY TRP SEQRES 2 A 523 ILE ASP SER THR SER PRO VAL ASN GLU GLN ILE THR ASN SEQRES 3 A 523 PRO ALA LEU VAL GLU GLN ILE TYR HIS SER ASN ASN ASP SEQRES 4 A 523 GLN LEU LEU TRP SER ASP LEU ALA THR ALA ASN HIS PHE SEQRES 5 A 523 GLU ALA GLN LEU GLU VAL ILE HIS ARG ALA SER PHE SER SEQRES 6 A 523 PRO LEU PHE SER ARG GLN LEU PHE ALA LEU LYS SER TYR SEQRES 7 A 523 ARG GLN GLN ASP ARG TRP HIS GLU TYR ASP VAL LEU ALA SEQRES 8 A 523 THR ASP THR LEU LEU GLN TYR LEU SER TYR ALA GLU GLN SEQRES 9 A 523 ALA PRO LYS VAL GLY ILE ALA TRP PHE PHE GLU GLY GLN SEQRES 10 A 523 LEU ASP GLN PRO LEU ALA PRO PRO SER GLU GLU ALA GLN SEQRES 11 A 523 LEU ALA LEU HIS MET ALA ILE GLY ASN GLN SER LEU ALA SEQRES 12 A 523 ARG LEU MET ASP GLU TYR THR PRO GLN ASP PRO ALA TYR SEQRES 13 A 523 GLN GLN LEU LEU GLN ALA TYR GLN SER LEU SER SER ILE SEQRES 14 A 523 GLU PHE ASN GLU VAL ALA LEU TYR GLU GLN MET GLU ARG SEQRES 15 A 523 LEU LYS ARG PRO GLY ASP PRO LEU SER HIS ARG GLU ALA SEQRES 16 A 523 LEU VAL GLN ARG LEU ALA LEU VAL ASN LEU ASP THR THR SEQRES 17 A 523 SER ILE LEU ASN ASP VAL ALA TYR TYR ASP ALA SER LEU SEQRES 18 A 523 GLU LYS PRO ILE LYS GLN PHE GLN LYS MET HIS GLY LEU SEQRES 19 A 523 GLN THR ASP GLY VAL ILE GLY PRO GLN THR MET LYS TRP SEQRES 20 A 523 LEU ASN THR SER VAL THR GLU ARG LEU ALA LEU LEU ALA SEQRES 21 A 523 LEU ASN ALA GLU ARG ILE ARG LEU TRP PRO THR GLN GLN SEQRES 22 A 523 ASP SER MET ILE VAL VAL ASN VAL PRO GLY PHE ASP MET SEQRES 23 A 523 LYS TYR TRP ASP ALA GLY ARG GLU VAL PHE GLU SER LYS SEQRES 24 A 523 VAL VAL VAL GLY LYS THR THR ARG PRO THR PRO VAL MET SEQRES 25 A 523 ASN THR LYS LEU ASP SER LEU ILE ILE ASN PRO THR TRP SEQRES 26 A 523 ASN VAL PRO HIS LYS ILE MET VAL GLU ASP ILE LEU PRO SEQRES 27 A 523 MET VAL LYS ARG ASP SER GLU TYR LEU ALA ASN HIS HIS SEQRES 28 A 523 MET GLU ILE ILE ARG GLY TRP SER ASP PRO GLU VAL ILE SEQRES 29 A 523 ASP PRO ALA LEU ILE ASP TRP GLU ALA VAL GLU PRO GLU SEQRES 30 A 523 THR PHE PRO TYR ARG LEU ARG GLN GLN ALA GLY VAL GLN SEQRES 31 A 523 ASN ALA LEU GLY THR TYR LYS PHE ASN THR PRO ASN SER SEQRES 32 A 523 ARG ALA ILE TYR LEU HIS ASP THR PRO SER LYS HIS LEU SEQRES 33 A 523 PHE ASN ASN ALA SER ARG ALA PHE SER SER GLY CYS ILE SEQRES 34 A 523 ARG VAL GLU ASN ALA GLU LYS PHE ALA GLN THR LEU LEU SEQRES 35 A 523 ALA ASN GLN GLY ILE THR LEU ASP ASP PHE PRO VAL SER SEQRES 36 A 523 THR GLN ALA ILE ALA LEU LYS LYS ARG ILE PRO VAL HIS SEQRES 37 A 523 ILE ILE TYR GLN THR VAL TRP TYR GLU GLU GLY VAL LEU SEQRES 38 A 523 HIS TYR ARG ASP ASP ILE TYR HIS TYR ASP ALA LEU ALA SEQRES 39 A 523 LEU GLY ASN GLY ASP ALA SER PRO ASN LEU THR LYS ILE SEQRES 40 A 523 GLU ASN LEU TYR PHE GLN GLY SER SER SER HIS HIS HIS SEQRES 41 A 523 HIS HIS HIS SEQRES 1 B 523 ALA ALA MET VAL THR GLN ARG PHE VAL GLU LEU GLY TRP SEQRES 2 B 523 ILE ASP SER THR SER PRO VAL ASN GLU GLN ILE THR ASN SEQRES 3 B 523 PRO ALA LEU VAL GLU GLN ILE TYR HIS SER ASN ASN ASP SEQRES 4 B 523 GLN LEU LEU TRP SER ASP LEU ALA THR ALA ASN HIS PHE SEQRES 5 B 523 GLU ALA GLN LEU GLU VAL ILE HIS ARG ALA SER PHE SER SEQRES 6 B 523 PRO LEU PHE SER ARG GLN LEU PHE ALA LEU LYS SER TYR SEQRES 7 B 523 ARG GLN GLN ASP ARG TRP HIS GLU TYR ASP VAL LEU ALA SEQRES 8 B 523 THR ASP THR LEU LEU GLN TYR LEU SER TYR ALA GLU GLN SEQRES 9 B 523 ALA PRO LYS VAL GLY ILE ALA TRP PHE PHE GLU GLY GLN SEQRES 10 B 523 LEU ASP GLN PRO LEU ALA PRO PRO SER GLU GLU ALA GLN SEQRES 11 B 523 LEU ALA LEU HIS MET ALA ILE GLY ASN GLN SER LEU ALA SEQRES 12 B 523 ARG LEU MET ASP GLU TYR THR PRO GLN ASP PRO ALA TYR SEQRES 13 B 523 GLN GLN LEU LEU GLN ALA TYR GLN SER LEU SER SER ILE SEQRES 14 B 523 GLU PHE ASN GLU VAL ALA LEU TYR GLU GLN MET GLU ARG SEQRES 15 B 523 LEU LYS ARG PRO GLY ASP PRO LEU SER HIS ARG GLU ALA SEQRES 16 B 523 LEU VAL GLN ARG LEU ALA LEU VAL ASN LEU ASP THR THR SEQRES 17 B 523 SER ILE LEU ASN ASP VAL ALA TYR TYR ASP ALA SER LEU SEQRES 18 B 523 GLU LYS PRO ILE LYS GLN PHE GLN LYS MET HIS GLY LEU SEQRES 19 B 523 GLN THR ASP GLY VAL ILE GLY PRO GLN THR MET LYS TRP SEQRES 20 B 523 LEU ASN THR SER VAL THR GLU ARG LEU ALA LEU LEU ALA SEQRES 21 B 523 LEU ASN ALA GLU ARG ILE ARG LEU TRP PRO THR GLN GLN SEQRES 22 B 523 ASP SER MET ILE VAL VAL ASN VAL PRO GLY PHE ASP MET SEQRES 23 B 523 LYS TYR TRP ASP ALA GLY ARG GLU VAL PHE GLU SER LYS SEQRES 24 B 523 VAL VAL VAL GLY LYS THR THR ARG PRO THR PRO VAL MET SEQRES 25 B 523 ASN THR LYS LEU ASP SER LEU ILE ILE ASN PRO THR TRP SEQRES 26 B 523 ASN VAL PRO HIS LYS ILE MET VAL GLU ASP ILE LEU PRO SEQRES 27 B 523 MET VAL LYS ARG ASP SER GLU TYR LEU ALA ASN HIS HIS SEQRES 28 B 523 MET GLU ILE ILE ARG GLY TRP SER ASP PRO GLU VAL ILE SEQRES 29 B 523 ASP PRO ALA LEU ILE ASP TRP GLU ALA VAL GLU PRO GLU SEQRES 30 B 523 THR PHE PRO TYR ARG LEU ARG GLN GLN ALA GLY VAL GLN SEQRES 31 B 523 ASN ALA LEU GLY THR TYR LYS PHE ASN THR PRO ASN SER SEQRES 32 B 523 ARG ALA ILE TYR LEU HIS ASP THR PRO SER LYS HIS LEU SEQRES 33 B 523 PHE ASN ASN ALA SER ARG ALA PHE SER SER GLY CYS ILE SEQRES 34 B 523 ARG VAL GLU ASN ALA GLU LYS PHE ALA GLN THR LEU LEU SEQRES 35 B 523 ALA ASN GLN GLY ILE THR LEU ASP ASP PHE PRO VAL SER SEQRES 36 B 523 THR GLN ALA ILE ALA LEU LYS LYS ARG ILE PRO VAL HIS SEQRES 37 B 523 ILE ILE TYR GLN THR VAL TRP TYR GLU GLU GLY VAL LEU SEQRES 38 B 523 HIS TYR ARG ASP ASP ILE TYR HIS TYR ASP ALA LEU ALA SEQRES 39 B 523 LEU GLY ASN GLY ASP ALA SER PRO ASN LEU THR LYS ILE SEQRES 40 B 523 GLU ASN LEU TYR PHE GLN GLY SER SER SER HIS HIS HIS SEQRES 41 B 523 HIS HIS HIS SEQRES 1 C 4 ALA DGL API DAL HET DGL C 3 8 HET API C 4 12 HET DAL C 5 6 HET EDO A 601 4 HET EDO B 601 4 HET AMV C 101 20 HETNAM DGL D-GLUTAMIC ACID HETNAM API 2,6-DIAMINOPIMELIC ACID HETNAM DAL D-ALANINE HETNAM EDO 1,2-ETHANEDIOL HETNAM AMV METHYL 2-ACETAMIDO-3-O-[(1R)-1-CARBOXYETHYL]-2-DEOXY- HETNAM 2 AMV BETA-D-GLUCOPYRANOSIDE HETSYN EDO ETHYLENE GLYCOL HETSYN AMV METHYL 2-(ACETYLAMINO)-3-O-[(1R)-1-CARBOXYETHYL]-2- HETSYN 2 AMV DEOXY-BETA-D-GLUCOPYRANOSIDE; METHYL 2-ACETAMIDO-3-O- HETSYN 3 AMV [(1R)-1-CARBOXYETHYL]-2-DEOXY-BETA-D-GLUCOSIDE; METHYL HETSYN 4 AMV 2-ACETAMIDO-3-O-[(1R)-1-CARBOXYETHYL]-2-DEOXY-D- HETSYN 5 AMV GLUCOSIDE; METHYL 2-ACETAMIDO-3-O-[(1R)-1- HETSYN 6 AMV CARBOXYETHYL]-2-DEOXY-GLUCOSIDE FORMUL 3 DGL C5 H9 N O4 FORMUL 3 API C7 H14 N2 O4 FORMUL 3 DAL C3 H7 N O2 FORMUL 4 EDO 2(C2 H6 O2) FORMUL 6 AMV C12 H21 N O8 FORMUL 7 HOH *24(H2 O) HELIX 1 AA1 PRO A 35 ILE A 40 1 6 HELIX 2 AA2 ASN A 42 SER A 52 1 11 HELIX 3 AA3 ASP A 61 ALA A 78 1 18 HELIX 4 AA4 SER A 81 GLN A 97 1 17 HELIX 5 AA5 ARG A 99 GLY A 125 1 27 HELIX 6 AA6 GLY A 125 PHE A 130 1 6 HELIX 7 AA7 SER A 142 ASN A 155 1 14 HELIX 8 AA8 SER A 157 TYR A 165 1 9 HELIX 9 AA9 ASP A 169 GLU A 186 1 18 HELIX 10 AB1 HIS A 208 LEU A 218 1 11 HELIX 11 AB2 ASP A 234 HIS A 248 1 15 HELIX 12 AB3 GLY A 257 THR A 266 1 10 HELIX 13 AB4 SER A 267 ILE A 282 1 16 HELIX 14 AB5 PRO A 344 ASP A 351 1 8 HELIX 15 AB6 ASP A 351 LYS A 357 1 7 HELIX 16 AB7 GLU A 361 HIS A 367 1 7 HELIX 17 AB8 ASP A 381 ILE A 385 5 5 HELIX 18 AB9 GLU A 391 PHE A 395 5 5 HELIX 19 AC1 SER A 429 ASN A 435 5 7 HELIX 20 AC2 ASN A 449 ASN A 460 1 12 HELIX 21 AC3 PRO B 35 ILE B 40 1 6 HELIX 22 AC4 ASN B 42 SER B 52 1 11 HELIX 23 AC5 ASP B 61 ALA B 78 1 18 HELIX 24 AC6 SER B 81 GLN B 97 1 17 HELIX 25 AC7 ARG B 99 GLY B 125 1 27 HELIX 26 AC8 GLY B 125 PHE B 130 1 6 HELIX 27 AC9 SER B 142 ASN B 155 1 14 HELIX 28 AD1 SER B 157 TYR B 165 1 9 HELIX 29 AD2 ASP B 169 ILE B 185 1 17 HELIX 30 AD3 HIS B 208 LEU B 218 1 11 HELIX 31 AD4 ASP B 234 HIS B 248 1 15 HELIX 32 AD5 GLY B 257 THR B 266 1 10 HELIX 33 AD6 SER B 267 ARG B 283 1 17 HELIX 34 AD7 PRO B 344 ASP B 351 1 8 HELIX 35 AD8 ASP B 351 LYS B 357 1 7 HELIX 36 AD9 GLU B 361 HIS B 367 1 7 HELIX 37 AE1 ASP B 381 ILE B 385 5 5 HELIX 38 AE2 GLU B 391 PHE B 395 5 5 HELIX 39 AE3 SER B 429 ASN B 435 5 7 HELIX 40 AE4 ASN B 449 ASN B 460 1 12 HELIX 41 AE5 ASP B 507 LEU B 511 5 5 SHEET 1 AA110 ALA A 439 SER A 441 0 SHEET 2 AA110 ARG A 309 GLY A 319 1 N VAL A 318 O SER A 441 SHEET 3 AA110 ILE A 445 VAL A 447 -1 O ARG A 446 N VAL A 317 SHEET 4 AA110 LEU A 424 HIS A 425 1 N HIS A 425 O VAL A 447 SHEET 5 AA110 TYR A 412 ASN A 415 -1 N PHE A 414 O LEU A 424 SHEET 6 AA110 MET A 328 ILE A 337 -1 N ILE A 336 O LYS A 413 SHEET 7 AA110 GLN A 473 ILE A 486 -1 O VAL A 483 N THR A 330 SHEET 8 AA110 SER A 291 ASN A 296 1 N ILE A 293 O HIS A 484 SHEET 9 AA110 ASP A 301 ASP A 306 -1 O TRP A 305 N MET A 292 SHEET 10 AA110 ARG A 309 GLY A 319 -1 O ARG A 309 N ASP A 306 SHEET 1 AA2 4 TRP A 341 ASN A 342 0 SHEET 2 AA2 4 ARG A 398 GLN A 401 -1 O GLN A 401 N TRP A 341 SHEET 3 AA2 4 MET A 368 ARG A 372 -1 N ILE A 371 O ARG A 398 SHEET 4 AA2 4 GLU A 378 ILE A 380 -1 O ILE A 380 N ILE A 370 SHEET 1 AA3 2 VAL A 490 GLU A 493 0 SHEET 2 AA3 2 VAL A 496 TYR A 499 -1 O VAL A 496 N GLU A 493 SHEET 1 AA410 ALA B 439 SER B 441 0 SHEET 2 AA410 ARG B 309 GLY B 319 1 N VAL B 318 O SER B 441 SHEET 3 AA410 ILE B 445 VAL B 447 -1 O ARG B 446 N VAL B 317 SHEET 4 AA410 LEU B 424 HIS B 425 1 N HIS B 425 O VAL B 447 SHEET 5 AA410 TYR B 412 ASN B 415 -1 N PHE B 414 O LEU B 424 SHEET 6 AA410 MET B 328 ILE B 337 -1 N ILE B 336 O LYS B 413 SHEET 7 AA410 GLN B 473 ILE B 486 -1 O VAL B 483 N THR B 330 SHEET 8 AA410 SER B 291 ASN B 296 1 N ILE B 293 O HIS B 484 SHEET 9 AA410 ASP B 301 ASP B 306 -1 O TRP B 305 N MET B 292 SHEET 10 AA410 ARG B 309 GLY B 319 -1 O ARG B 309 N ASP B 306 SHEET 1 AA5 4 TRP B 341 ASN B 342 0 SHEET 2 AA5 4 ARG B 398 GLN B 401 -1 O GLN B 401 N TRP B 341 SHEET 3 AA5 4 MET B 368 ILE B 371 -1 N ILE B 371 O ARG B 398 SHEET 4 AA5 4 VAL B 379 ILE B 380 -1 O ILE B 380 N ILE B 370 SHEET 1 AA6 2 VAL B 490 GLU B 493 0 SHEET 2 AA6 2 VAL B 496 TYR B 499 -1 O VAL B 496 N GLU B 493 LINK C ALA C 2 N DGL C 3 1555 1555 1.35 LINK N ALA C 2 C10 AMV C 101 1555 1555 1.36 LINK CD DGL C 3 N API C 4 1555 1555 1.33 LINK C API C 4 N DAL C 5 1555 1555 1.34 CRYST1 57.510 92.558 276.064 90.00 90.00 90.00 P 21 21 21 8 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 0.017388 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010804 0.000000 0.00000 SCALE3 0.000000 0.000000 0.003622 0.00000