HEADER TRANSFERASE 15-JUN-16 5LB1 TITLE CRYSTAL STRUCTURE OF THE MYCOBACTERIUM TUBERCULOSIS L,D- TITLE 2 TRANSPEPTIDASE-2 (LDTMT2) BC-MODULE WITH THIONITROBENZOATE (TNB) TITLE 3 ADDUCT AT THE ACTIVE SITE CYSTEINE-354 COMPND MOL_ID: 1; COMPND 2 MOLECULE: L,D-TRANSPEPTIDASE 2; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: UNP RESIDUES 149-408; COMPND 5 SYNONYM: LDT 2,LDT(MT2); COMPND 6 EC: 2.3.2.-; COMPND 7 ENGINEERED: YES; COMPND 8 OTHER_DETAILS: COVALENT ADDUCT (THIO-NITRO-BENZOATE) ON CYS354, MIXED COMPND 9 DISULPHIDE BOND SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MYCOBACTERIUM TUBERCULOSIS; SOURCE 3 ORGANISM_TAXID: 83332; SOURCE 4 STRAIN: ATCC 25618 / H37RV; SOURCE 5 GENE: LDTB, LPPS, RV2518C, RVBD_2518C, P425_02624; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PNIC28BSA4 KEYWDS CELL WALL, PEPTIDOGLYCAN, TRANSPEPTIDASE, MYCOBACTERIUM TUBERCULOSIS, KEYWDS 2 TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR E.M.STEINER,R.SCHNELL,G.SCHNEIDER REVDAT 3 10-JAN-24 5LB1 1 REMARK REVDAT 2 15-MAR-17 5LB1 1 JRNL REVDAT 1 18-JAN-17 5LB1 0 JRNL AUTH E.M.STEINER,G.SCHNEIDER,R.SCHNELL JRNL TITL BINDING AND PROCESSING OF BETA-LACTAM ANTIBIOTICS BY THE JRNL TITL 2 TRANSPEPTIDASE LDTMT2 FROM MYCOBACTERIUM TUBERCULOSIS. JRNL REF FEBS J. V. 284 725 2017 JRNL REFN ISSN 1742-4658 JRNL PMID 28075068 JRNL DOI 10.1111/FEBS.14010 REMARK 2 REMARK 2 RESOLUTION. 1.55 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.7.0029 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) : 1.55 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 51.40 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 95.4 REMARK 3 NUMBER OF REFLECTIONS : 75507 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) : 0.150 REMARK 3 R VALUE (WORKING SET) : 0.147 REMARK 3 FREE R VALUE : 0.194 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 3953 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) : 1.55 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.59 REMARK 3 REFLECTION IN BIN (WORKING SET) : 5388 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 91.00 REMARK 3 BIN R VALUE (WORKING SET) : 0.2670 REMARK 3 BIN FREE R VALUE SET COUNT : 255 REMARK 3 BIN FREE R VALUE : 0.3450 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3935 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 26 REMARK 3 SOLVENT ATOMS : 672 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 11.20 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 14.58 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.20000 REMARK 3 B22 (A**2) : -0.06000 REMARK 3 B33 (A**2) : 0.14000 REMARK 3 B12 (A**2) : 0.12000 REMARK 3 B13 (A**2) : -0.03000 REMARK 3 B23 (A**2) : -0.12000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.091 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.078 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.049 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.013 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.967 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): 4247 ; 0.011 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 3835 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5836 ; 1.453 ; 1.921 REMARK 3 BOND ANGLES OTHERS (DEGREES): 8815 ; 0.879 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 545 ; 5.914 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 194 ;30.654 ;24.072 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 621 ;11.820 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 24 ;17.177 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 626 ; 0.090 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5019 ; 0.007 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 1019 ; 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): 8082 ; 4.279 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 190 ;29.813 ; 5.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 8434 ; 8.580 ; 5.000 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 : 1.20 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 5LB1 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 15-JUN-16. REMARK 100 THE DEPOSITION ID IS D_1200000447. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-NOV-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID23-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.8726 REMARK 200 MONOCHROMATOR : SI (111) MONOCHROMATOR REMARK 200 OPTICS : PT COATED MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 2M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 79462 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.550 REMARK 200 RESOLUTION RANGE LOW (A) : 51.400 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.700 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.3 REMARK 200 DATA REDUNDANCY : 2.000 REMARK 200 R MERGE (I) : 0.06500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.55 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.57 REMARK 200 COMPLETENESS FOR SHELL (%) : 89.6 REMARK 200 DATA REDUNDANCY IN SHELL : 2.00 REMARK 200 R MERGE FOR SHELL (I) : 0.37900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 4HUC REMARK 200 REMARK 200 REMARK: SPEAR TIP REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.70 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.60 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M MES/IMIDAZOL PH 6.5 0.02M OF EACH REMARK 280 CARBOXYLIC ACID (SODIUM FORMATE, AMMONIUM ACETATE, TRI-SODIUM REMARK 280 CITRATE, SODIUM POTASSIUM DL-TARTRATE, SODIUM OXAMATE) 10% PEG REMARK 280 20000 20%PEGMME 550, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 293K 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: MONOMERIC 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: 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 SER A 147 REMARK 465 MET A 148 REMARK 465 ALA A 149 REMARK 465 ALA A 408 REMARK 465 GLY B 309 REMARK 465 VAL B 310 REMARK 465 PRO B 311 REMARK 465 VAL B 312 REMARK 465 ASN B 313 REMARK 465 SER B 314 REMARK 465 PRO B 315 REMARK 465 ASN B 316 REMARK 465 ALA B 408 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 745 O HOH B 887 1.92 REMARK 500 O HOH B 602 O HOH B 745 2.10 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 O HOH A 644 O HOH B 857 1556 2.07 REMARK 500 O HOH A 841 O HOH B 896 1556 2.12 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 ASN A 204 -167.95 -172.84 REMARK 500 ASN A 227 59.29 -101.36 REMARK 500 MET A 280 -165.21 -102.36 REMARK 500 HIS A 347 -52.21 -135.04 REMARK 500 HIS A 347 -55.11 -135.04 REMARK 500 ASN A 405 37.29 -146.57 REMARK 500 ASN B 227 57.37 -97.68 REMARK 500 MET B 280 -163.49 -107.30 REMARK 500 HIS B 347 -54.49 -136.18 REMARK 500 ASN B 405 39.90 -143.54 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 943 DISTANCE = 5.84 ANGSTROMS REMARK 525 HOH A 944 DISTANCE = 5.99 ANGSTROMS REMARK 525 HOH A 945 DISTANCE = 6.37 ANGSTROMS REMARK 525 HOH A 946 DISTANCE = 6.44 ANGSTROMS REMARK 525 HOH A 947 DISTANCE = 6.50 ANGSTROMS REMARK 525 HOH B 924 DISTANCE = 7.99 ANGSTROMS REMARK 525 HOH B 925 DISTANCE = 9.98 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MNB A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-peptide MNB B 501 and CYS B REMARK 800 354 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4HUC RELATED DB: PDB REMARK 900 LIGAND FREE STRUCTURE OF THE SAME PROTEIN. DBREF 5LB1 A 149 408 UNP I6Y9J2 LDT2_MYCTU 149 408 DBREF 5LB1 B 149 408 UNP I6Y9J2 LDT2_MYCTU 149 408 SEQADV 5LB1 SER A 147 UNP I6Y9J2 EXPRESSION TAG SEQADV 5LB1 MET A 148 UNP I6Y9J2 EXPRESSION TAG SEQADV 5LB1 SER B 147 UNP I6Y9J2 EXPRESSION TAG SEQADV 5LB1 MET B 148 UNP I6Y9J2 EXPRESSION TAG SEQRES 1 A 262 SER MET ALA HIS LEU THR MET PRO TYR VAL MET PRO GLY SEQRES 2 A 262 ASP GLY GLU VAL VAL GLY VAL GLY GLU PRO VAL ALA ILE SEQRES 3 A 262 ARG PHE ASP GLU ASN ILE ALA ASP ARG GLY ALA ALA GLU SEQRES 4 A 262 LYS ALA ILE LYS ILE THR THR ASN PRO PRO VAL GLU GLY SEQRES 5 A 262 ALA PHE TYR TRP LEU ASN ASN ARG GLU VAL ARG TRP ARG SEQRES 6 A 262 PRO GLU HIS PHE TRP LYS PRO GLY THR ALA VAL ASP VAL SEQRES 7 A 262 ALA VAL ASN THR TYR GLY VAL ASP LEU GLY GLU GLY MET SEQRES 8 A 262 PHE GLY GLU ASP ASN VAL GLN THR HIS PHE THR ILE GLY SEQRES 9 A 262 ASP GLU VAL ILE ALA THR ALA ASP ASP ASN THR LYS ILE SEQRES 10 A 262 LEU THR VAL ARG VAL ASN GLY GLU VAL VAL LYS SER MET SEQRES 11 A 262 PRO THR SER MET GLY LYS ASP SER THR PRO THR ALA ASN SEQRES 12 A 262 GLY ILE TYR ILE VAL GLY SER ARG TYR LYS HIS ILE ILE SEQRES 13 A 262 MET ASP SER SER THR TYR GLY VAL PRO VAL ASN SER PRO SEQRES 14 A 262 ASN GLY TYR ARG THR ASP VAL ASP TRP ALA THR GLN ILE SEQRES 15 A 262 SER TYR SER GLY VAL PHE VAL HIS SER ALA PRO TRP SER SEQRES 16 A 262 VAL GLY ALA GLN GLY HIS THR ASN THR SER HIS GLY CYS SEQRES 17 A 262 LEU ASN VAL SER PRO SER ASN ALA GLN TRP PHE TYR ASP SEQRES 18 A 262 HIS VAL LYS ARG GLY ASP ILE VAL GLU VAL VAL ASN THR SEQRES 19 A 262 VAL GLY GLY THR LEU PRO GLY ILE ASP GLY LEU GLY ASP SEQRES 20 A 262 TRP ASN ILE PRO TRP ASP GLN TRP ARG ALA GLY ASN ALA SEQRES 21 A 262 LYS ALA SEQRES 1 B 262 SER MET ALA HIS LEU THR MET PRO TYR VAL MET PRO GLY SEQRES 2 B 262 ASP GLY GLU VAL VAL GLY VAL GLY GLU PRO VAL ALA ILE SEQRES 3 B 262 ARG PHE ASP GLU ASN ILE ALA ASP ARG GLY ALA ALA GLU SEQRES 4 B 262 LYS ALA ILE LYS ILE THR THR ASN PRO PRO VAL GLU GLY SEQRES 5 B 262 ALA PHE TYR TRP LEU ASN ASN ARG GLU VAL ARG TRP ARG SEQRES 6 B 262 PRO GLU HIS PHE TRP LYS PRO GLY THR ALA VAL ASP VAL SEQRES 7 B 262 ALA VAL ASN THR TYR GLY VAL ASP LEU GLY GLU GLY MET SEQRES 8 B 262 PHE GLY GLU ASP ASN VAL GLN THR HIS PHE THR ILE GLY SEQRES 9 B 262 ASP GLU VAL ILE ALA THR ALA ASP ASP ASN THR LYS ILE SEQRES 10 B 262 LEU THR VAL ARG VAL ASN GLY GLU VAL VAL LYS SER MET SEQRES 11 B 262 PRO THR SER MET GLY LYS ASP SER THR PRO THR ALA ASN SEQRES 12 B 262 GLY ILE TYR ILE VAL GLY SER ARG TYR LYS HIS ILE ILE SEQRES 13 B 262 MET ASP SER SER THR TYR GLY VAL PRO VAL ASN SER PRO SEQRES 14 B 262 ASN GLY TYR ARG THR ASP VAL ASP TRP ALA THR GLN ILE SEQRES 15 B 262 SER TYR SER GLY VAL PHE VAL HIS SER ALA PRO TRP SER SEQRES 16 B 262 VAL GLY ALA GLN GLY HIS THR ASN THR SER HIS GLY CYS SEQRES 17 B 262 LEU ASN VAL SER PRO SER ASN ALA GLN TRP PHE TYR ASP SEQRES 18 B 262 HIS VAL LYS ARG GLY ASP ILE VAL GLU VAL VAL ASN THR SEQRES 19 B 262 VAL GLY GLY THR LEU PRO GLY ILE ASP GLY LEU GLY ASP SEQRES 20 B 262 TRP ASN ILE PRO TRP ASP GLN TRP ARG ALA GLY ASN ALA SEQRES 21 B 262 LYS ALA HET MNB A 501 13 HET MNB B 501 13 HETNAM MNB 5-MERCAPTO-2-NITRO-BENZOIC ACID FORMUL 3 MNB 2(C7 H5 N O4 S) FORMUL 5 HOH *672(H2 O) HELIX 1 AA1 ASP A 180 ALA A 187 1 8 HELIX 2 AA2 SER A 306 GLY A 309 5 4 HELIX 3 AA3 PRO A 339 VAL A 342 5 4 HELIX 4 AA4 SER A 358 VAL A 369 1 12 HELIX 5 AA5 GLY A 392 ILE A 396 5 5 HELIX 6 AA6 PRO A 397 GLY A 404 1 8 HELIX 7 AA7 ASP B 180 ALA B 187 1 8 HELIX 8 AA8 SER B 306 TYR B 308 5 3 HELIX 9 AA9 PRO B 339 VAL B 342 5 4 HELIX 10 AB1 SER B 358 VAL B 369 1 12 HELIX 11 AB2 GLY B 392 ILE B 396 5 5 HELIX 12 AB3 PRO B 397 GLY B 404 1 8 SHEET 1 AA1 2 LEU A 151 THR A 152 0 SHEET 2 AA1 2 PHE A 238 GLY A 239 1 O PHE A 238 N THR A 152 SHEET 1 AA2 4 PRO A 154 MET A 157 0 SHEET 2 AA2 4 VAL A 170 PHE A 174 -1 O ALA A 171 N MET A 157 SHEET 3 AA2 4 GLU A 207 PRO A 212 -1 O VAL A 208 N ILE A 172 SHEET 4 AA2 4 GLY A 198 TRP A 202 -1 N TYR A 201 O ARG A 209 SHEET 1 AA3 4 VAL A 163 VAL A 164 0 SHEET 2 AA3 4 VAL A 243 ILE A 249 1 O THR A 248 N VAL A 164 SHEET 3 AA3 4 ALA A 221 VAL A 226 -1 N VAL A 226 O VAL A 243 SHEET 4 AA3 4 ILE A 188 ASN A 193 -1 N ASN A 193 O ALA A 221 SHEET 1 AA4 5 GLU A 271 PRO A 277 0 SHEET 2 AA4 5 ILE A 263 VAL A 268 -1 N LEU A 264 O MET A 276 SHEET 3 AA4 5 VAL A 253 ASP A 258 -1 N THR A 256 O THR A 265 SHEET 4 AA4 5 ILE A 374 VAL A 378 1 O GLU A 376 N ALA A 255 SHEET 5 AA4 5 GLY A 290 ILE A 293 -1 N TYR A 292 O VAL A 375 SHEET 1 AA5 4 ARG A 297 ASP A 304 0 SHEET 2 AA5 4 ARG A 319 GLN A 327 -1 O ALA A 325 N TYR A 298 SHEET 3 AA5 4 PHE A 334 SER A 337 -1 O VAL A 335 N THR A 326 SHEET 4 AA5 4 LEU A 355 VAL A 357 1 O LEU A 355 N PHE A 334 SHEET 1 AA6 2 LEU B 151 THR B 152 0 SHEET 2 AA6 2 PHE B 238 GLY B 239 1 O PHE B 238 N THR B 152 SHEET 1 AA7 4 PRO B 154 MET B 157 0 SHEET 2 AA7 4 VAL B 170 PHE B 174 -1 O ARG B 173 N TYR B 155 SHEET 3 AA7 4 GLU B 207 PRO B 212 -1 O VAL B 208 N ILE B 172 SHEET 4 AA7 4 GLY B 198 TRP B 202 -1 N TYR B 201 O ARG B 209 SHEET 1 AA8 4 VAL B 163 VAL B 164 0 SHEET 2 AA8 4 VAL B 243 ILE B 249 1 O THR B 248 N VAL B 164 SHEET 3 AA8 4 ALA B 221 VAL B 226 -1 N VAL B 224 O THR B 245 SHEET 4 AA8 4 ILE B 188 ASN B 193 -1 N LYS B 189 O ALA B 225 SHEET 1 AA9 5 GLU B 271 PRO B 277 0 SHEET 2 AA9 5 ILE B 263 VAL B 268 -1 N LEU B 264 O MET B 276 SHEET 3 AA9 5 VAL B 253 ASP B 258 -1 N ILE B 254 O ARG B 267 SHEET 4 AA9 5 ILE B 374 VAL B 378 1 O GLU B 376 N ALA B 257 SHEET 5 AA9 5 GLY B 290 ILE B 293 -1 N TYR B 292 O VAL B 375 SHEET 1 AB1 4 ARG B 297 ASP B 304 0 SHEET 2 AB1 4 ARG B 319 GLN B 327 -1 O THR B 320 N MET B 303 SHEET 3 AB1 4 PHE B 334 SER B 337 -1 O VAL B 335 N THR B 326 SHEET 4 AB1 4 LEU B 355 VAL B 357 1 O LEU B 355 N PHE B 334 LINK SG CYS A 354 S5 MNB A 501 1555 1555 1.99 LINK SG CYS B 354 S5 MNB B 501 1555 1555 2.02 CISPEP 1 MET A 157 PRO A 158 0 -0.36 CISPEP 2 ASN A 193 PRO A 194 0 3.45 CISPEP 3 MET B 157 PRO B 158 0 4.42 CISPEP 4 ASN B 193 PRO B 194 0 7.43 SITE 1 AC1 10 TYR A 308 TYR A 318 THR A 320 HIS A 336 SITE 2 AC1 10 TRP A 340 CYS A 354 HOH A 694 HOH A 709 SITE 3 AC1 10 HOH A 744 HOH A 788 SITE 1 AC2 15 SER B 279 MET B 280 ASP B 304 TYR B 308 SITE 2 AC2 15 TYR B 318 THR B 320 GLY B 332 PHE B 334 SITE 3 AC2 15 HIS B 336 SER B 351 HIS B 352 GLY B 353 SITE 4 AC2 15 LEU B 355 ASN B 356 HOH B 790 CRYST1 53.368 53.910 57.174 68.84 75.03 88.64 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 0.018738 -0.000446 -0.005213 0.00000 SCALE2 0.000000 0.018555 -0.007331 0.00000 SCALE3 0.000000 0.000000 0.019467 0.00000