HEADER PEPTIDOGLYCAN BINDING PROTEIN 30-SEP-11 3U1P TITLE CRYSTAL STRUCTURE OF M. TUBERCULOSIS LD-TRANSPEPTIDASE TYPE 2 WITH TITLE 2 MODIFIED CATALYTIC CYSTEINE (C354) COMPND MOL_ID: 1; COMPND 2 MOLECULE: MYCOBACTERIA TUBERCULOSIS LD-TRANSPEPTIDASE TYPE 2; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MYCOBACTERIUM TUBERCULOSIS; SOURCE 3 ORGANISM_TAXID: 1773; SOURCE 4 GENE: LPPS, MT2594, RV2518C; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID KEYWDS PROTEIN-PEPTIDOGLYCAN COMPLEX, PEPTIDOGLYCAN BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR S.ERDEMLI,M.A.BIANCHET,R.GUPTA,G.LAMICHHANE,L.M.AMZEL REVDAT 4 04-APR-18 3U1P 1 REMARK REVDAT 3 26-DEC-12 3U1P 1 JRNL REVDAT 2 12-DEC-12 3U1P 1 JRNL REVDAT 1 05-DEC-12 3U1P 0 JRNL AUTH S.B.ERDEMLI,R.GUPTA,W.R.BISHAI,G.LAMICHHANE,L.M.AMZEL, JRNL AUTH 2 M.A.BIANCHET JRNL TITL TARGETING THE CELL WALL OF MYCOBACTERIUM TUBERCULOSIS: JRNL TITL 2 STRUCTURE AND MECHANISM OF L,D-TRANSPEPTIDASE 2. JRNL REF STRUCTURE V. 20 2103 2012 JRNL REFN ISSN 0969-2126 JRNL PMID 23103390 JRNL DOI 10.1016/J.STR.2012.09.016 REMARK 2 REMARK 2 RESOLUTION. 2.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0072 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) : 2.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.84 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 22139 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) : 0.190 REMARK 3 R VALUE (WORKING SET) : 0.187 REMARK 3 FREE R VALUE : 0.258 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1127 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) : 2.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.87 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1487 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.43 REMARK 3 BIN R VALUE (WORKING SET) : 0.2870 REMARK 3 BIN FREE R VALUE SET COUNT : 85 REMARK 3 BIN FREE R VALUE : 0.4140 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4029 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 14 REMARK 3 SOLVENT ATOMS : 154 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.82 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.18000 REMARK 3 B22 (A**2) : -0.85000 REMARK 3 B33 (A**2) : -1.33000 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): 0.331 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.228 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 11.339 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.928 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.861 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4202 ; 0.017 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5749 ; 1.730 ; 1.917 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 539 ;10.150 ; 5.074 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 195 ;33.962 ;24.308 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 610 ;18.267 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 22 ;20.190 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 621 ; 0.112 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3296 ; 0.008 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 2613 ; 0.729 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4242 ; 1.443 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1589 ; 2.333 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1501 ; 4.010 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 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 3U1P COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-OCT-11. REMARK 100 THE DEPOSITION ID IS D_1000068194. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 2009 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : OTHER REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : VARIMAX REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RIGAKU SATURN 944+ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 22155 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.800 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 7.200 REMARK 200 R MERGE (I) : 0.15200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 4.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.85 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.5 REMARK 200 DATA REDUNDANCY IN SHELL : 6.20 REMARK 200 R MERGE FOR SHELL (I) : 0.55500 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: SHARP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 65.44 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.56 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M HEPES (PH 7.5), 1 M SUCCINIC REMARK 280 ACID, 1% (W/V) PEG MME 2000, TEMPERATURE 298K, VAPOR DIFFUSION, REMARK 280 HANGING DROP REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 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 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X,-Y+1/2,Z REMARK 290 7555 -X+1/2,Y,-Z REMARK 290 8555 X,-Y,-Z+1/2 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 59.52200 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 61.44200 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 60.61150 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 61.44200 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 59.52200 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 60.61150 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 59.52200 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 60.61150 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 61.44200 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 60.61150 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 59.52200 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 61.44200 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3 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 350 REMARK 350 BIOMOLECULE: 3 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1860 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 22520 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -7.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 ARG A 122 REMARK 465 LEU A 131 REMARK 465 GLY A 132 REMARK 465 LEU A 133 REMARK 465 GLY A 134 REMARK 465 GLY A 135 REMARK 465 ALA A 136 REMARK 465 ALA A 137 REMARK 465 THR A 138 REMARK 465 ARG A 139 REMARK 465 GLN A 140 REMARK 465 LEU A 141 REMARK 465 THR A 142 REMARK 465 PHE A 143 REMARK 465 GLN A 144 REMARK 465 THR A 145 REMARK 465 SER A 146 REMARK 465 SER A 147 REMARK 465 PRO A 148 REMARK 465 ALA A 149 REMARK 465 ALA A 408 REMARK 465 ARG B 122 REMARK 465 ARG B 123 REMARK 465 TYR B 124 REMARK 465 THR B 125 REMARK 465 LEU B 126 REMARK 465 ASN B 127 REMARK 465 ALA B 128 REMARK 465 THR B 129 REMARK 465 ALA B 130 REMARK 465 LEU B 131 REMARK 465 GLY B 132 REMARK 465 LEU B 133 REMARK 465 GLY B 134 REMARK 465 GLY B 135 REMARK 465 ALA B 136 REMARK 465 ALA B 137 REMARK 465 THR B 138 REMARK 465 ARG B 139 REMARK 465 GLN B 140 REMARK 465 LEU B 141 REMARK 465 THR B 142 REMARK 465 PHE B 143 REMARK 465 GLN B 144 REMARK 465 THR B 145 REMARK 465 SER B 146 REMARK 465 SER B 147 REMARK 465 PRO B 148 REMARK 465 ALA B 149 REMARK 465 ALA B 408 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 ARG A 123 CG CD NE CZ NH1 NH2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ASP A 258 CB - CG - OD2 ANGL. DEV. = -5.4 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 VAL A 166 -5.62 -58.77 REMARK 500 ASP A 180 77.38 -108.04 REMARK 500 ASN A 204 -161.70 -163.39 REMARK 500 VAL A 272 107.21 -56.00 REMARK 500 TRP A 394 0.46 -69.82 REMARK 500 ASP A 399 -46.05 135.22 REMARK 500 ASP A 399 -51.31 138.41 REMARK 500 ARG A 402 -60.82 -28.97 REMARK 500 ASN A 405 43.67 -144.36 REMARK 500 ASN B 227 78.56 -100.36 REMARK 500 GLU B 235 34.01 72.41 REMARK 500 THR B 285 65.23 -153.99 REMARK 500 ASN B 405 52.55 -156.78 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 PEG A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PEG B 501 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3TX4 RELATED DB: PDB REMARK 900 RELATED ID: 3TUR RELATED DB: PDB REMARK 900 RELATED ID: 3U1Q RELATED DB: PDB REMARK 900 RELATED ID: 3VAE RELATED DB: PDB DBREF 3U1P A 122 408 UNP O53223 O53223_MYCTU 122 408 DBREF 3U1P B 122 408 UNP O53223 O53223_MYCTU 122 408 SEQRES 1 A 287 ARG ARG TYR THR LEU ASN ALA THR ALA LEU GLY LEU GLY SEQRES 2 A 287 GLY ALA ALA THR ARG GLN LEU THR PHE GLN THR SER SER SEQRES 3 A 287 PRO ALA HIS LEU THR MET PRO TYR VAL MET PRO GLY ASP SEQRES 4 A 287 GLY GLU VAL VAL GLY VAL GLY GLU PRO VAL ALA ILE ARG SEQRES 5 A 287 PHE ASP GLU ASN ILE ALA ASP ARG GLY ALA ALA GLU LYS SEQRES 6 A 287 ALA ILE LYS ILE THR THR ASN PRO PRO VAL GLU GLY ALA SEQRES 7 A 287 PHE TYR TRP LEU ASN ASN ARG GLU VAL ARG TRP ARG PRO SEQRES 8 A 287 GLU HIS PHE TRP LYS PRO GLY THR ALA VAL ASP VAL ALA SEQRES 9 A 287 VAL ASN THR TYR GLY VAL ASP LEU GLY GLU GLY MET PHE SEQRES 10 A 287 GLY GLU ASP ASN VAL GLN THR HIS PHE THR ILE GLY ASP SEQRES 11 A 287 GLU VAL ILE ALA THR ALA ASP ASP ASN THR LYS ILE LEU SEQRES 12 A 287 THR VAL ARG VAL ASN GLY GLU VAL VAL LYS SER MET PRO SEQRES 13 A 287 THR SER MET GLY LYS ASP SER THR PRO THR ALA ASN GLY SEQRES 14 A 287 ILE TYR ILE VAL GLY SER ARG TYR LYS HIS ILE ILE MET SEQRES 15 A 287 ASP SER SER THR TYR GLY VAL PRO VAL ASN SER PRO ASN SEQRES 16 A 287 GLY TYR ARG THR ASP VAL ASP TRP ALA THR GLN ILE SER SEQRES 17 A 287 TYR SER GLY VAL PHE VAL HIS SER ALA PRO TRP SER VAL SEQRES 18 A 287 GLY ALA GLN GLY HIS THR ASN THR SER HIS GLY CSO LEU SEQRES 19 A 287 ASN VAL SER PRO SER ASN ALA GLN TRP PHE TYR ASP HIS SEQRES 20 A 287 VAL LYS ARG GLY ASP ILE VAL GLU VAL VAL ASN THR VAL SEQRES 21 A 287 GLY GLY THR LEU PRO GLY ILE ASP GLY LEU GLY ASP TRP SEQRES 22 A 287 ASN ILE PRO TRP ASP GLN TRP ARG ALA GLY ASN ALA LYS SEQRES 23 A 287 ALA SEQRES 1 B 287 ARG ARG TYR THR LEU ASN ALA THR ALA LEU GLY LEU GLY SEQRES 2 B 287 GLY ALA ALA THR ARG GLN LEU THR PHE GLN THR SER SER SEQRES 3 B 287 PRO ALA HIS LEU THR MET PRO TYR VAL MET PRO GLY ASP SEQRES 4 B 287 GLY GLU VAL VAL GLY VAL GLY GLU PRO VAL ALA ILE ARG SEQRES 5 B 287 PHE ASP GLU ASN ILE ALA ASP ARG GLY ALA ALA GLU LYS SEQRES 6 B 287 ALA ILE LYS ILE THR THR ASN PRO PRO VAL GLU GLY ALA SEQRES 7 B 287 PHE TYR TRP LEU ASN ASN ARG GLU VAL ARG TRP ARG PRO SEQRES 8 B 287 GLU HIS PHE TRP LYS PRO GLY THR ALA VAL ASP VAL ALA SEQRES 9 B 287 VAL ASN THR TYR GLY VAL ASP LEU GLY GLU GLY MET PHE SEQRES 10 B 287 GLY GLU ASP ASN VAL GLN THR HIS PHE THR ILE GLY ASP SEQRES 11 B 287 GLU VAL ILE ALA THR ALA ASP ASP ASN THR LYS ILE LEU SEQRES 12 B 287 THR VAL ARG VAL ASN GLY GLU VAL VAL LYS SER MET PRO SEQRES 13 B 287 THR SER MET GLY LYS ASP SER THR PRO THR ALA ASN GLY SEQRES 14 B 287 ILE TYR ILE VAL GLY SER ARG TYR LYS HIS ILE ILE MET SEQRES 15 B 287 ASP SER SER THR TYR GLY VAL PRO VAL ASN SER PRO ASN SEQRES 16 B 287 GLY TYR ARG THR ASP VAL ASP TRP ALA THR GLN ILE SER SEQRES 17 B 287 TYR SER GLY VAL PHE VAL HIS SER ALA PRO TRP SER VAL SEQRES 18 B 287 GLY ALA GLN GLY HIS THR ASN THR SER HIS GLY CSO LEU SEQRES 19 B 287 ASN VAL SER PRO SER ASN ALA GLN TRP PHE TYR ASP HIS SEQRES 20 B 287 VAL LYS ARG GLY ASP ILE VAL GLU VAL VAL ASN THR VAL SEQRES 21 B 287 GLY GLY THR LEU PRO GLY ILE ASP GLY LEU GLY ASP TRP SEQRES 22 B 287 ASN ILE PRO TRP ASP GLN TRP ARG ALA GLY ASN ALA LYS SEQRES 23 B 287 ALA MODRES 3U1P CSO A 354 CYS S-HYDROXYCYSTEINE MODRES 3U1P CSO B 354 CYS S-HYDROXYCYSTEINE HET CSO A 354 7 HET CSO B 354 7 HET PEG A 501 7 HET PEG B 501 7 HETNAM CSO S-HYDROXYCYSTEINE HETNAM PEG DI(HYDROXYETHYL)ETHER FORMUL 1 CSO 2(C3 H7 N O3 S) FORMUL 3 PEG 2(C4 H10 O3) FORMUL 5 HOH *154(H2 O) HELIX 1 1 ASP A 180 ALA A 187 1 8 HELIX 2 2 SER A 306 GLY A 309 5 4 HELIX 3 3 PRO A 339 VAL A 342 5 4 HELIX 4 4 SER A 358 VAL A 369 1 12 HELIX 5 5 GLY A 392 ILE A 396 5 5 HELIX 6 6 ASP A 399 GLY A 404 1 6 HELIX 7 7 ASP B 180 ALA B 187 1 8 HELIX 8 8 SER B 306 GLY B 309 5 4 HELIX 9 9 PRO B 339 GLN B 345 5 7 HELIX 10 10 SER B 358 VAL B 369 1 12 HELIX 11 11 GLY B 392 ILE B 396 5 5 HELIX 12 12 PRO B 397 GLY B 404 1 8 SHEET 1 A 4 PRO A 154 MET A 157 0 SHEET 2 A 4 VAL A 170 PHE A 174 -1 O ALA A 171 N MET A 157 SHEET 3 A 4 GLU A 207 PRO A 212 -1 O TRP A 210 N VAL A 170 SHEET 4 A 4 GLY A 198 TRP A 202 -1 N TYR A 201 O ARG A 209 SHEET 1 B 4 VAL A 163 VAL A 164 0 SHEET 2 B 4 VAL A 243 ILE A 249 1 O THR A 248 N VAL A 164 SHEET 3 B 4 ALA A 221 VAL A 226 -1 N VAL A 226 O VAL A 243 SHEET 4 B 4 ILE A 188 ASN A 193 -1 N LYS A 189 O ALA A 225 SHEET 1 C 5 GLU A 271 PRO A 277 0 SHEET 2 C 5 ILE A 263 VAL A 268 -1 N LEU A 264 O MET A 276 SHEET 3 C 5 VAL A 253 ASP A 258 -1 N THR A 256 O THR A 265 SHEET 4 C 5 ILE A 374 VAL A 378 1 O ILE A 374 N ALA A 255 SHEET 5 C 5 GLY A 290 ILE A 293 -1 N TYR A 292 O VAL A 375 SHEET 1 D 4 ARG A 297 ASP A 304 0 SHEET 2 D 4 ARG A 319 GLN A 327 -1 O VAL A 322 N ILE A 301 SHEET 3 D 4 PHE A 334 SER A 337 -1 O VAL A 335 N THR A 326 SHEET 4 D 4 LEU A 355 VAL A 357 1 O LEU A 355 N PHE A 334 SHEET 1 E 2 LEU B 151 THR B 152 0 SHEET 2 E 2 PHE B 238 GLY B 239 1 O PHE B 238 N THR B 152 SHEET 1 F 4 PRO B 154 MET B 157 0 SHEET 2 F 4 VAL B 170 PHE B 174 -1 O ALA B 171 N MET B 157 SHEET 3 F 4 GLU B 207 PRO B 212 -1 O VAL B 208 N ILE B 172 SHEET 4 F 4 GLY B 198 ASN B 204 -1 N TYR B 201 O ARG B 209 SHEET 1 G 4 VAL B 163 VAL B 164 0 SHEET 2 G 4 ASN B 242 ILE B 249 1 O THR B 248 N VAL B 164 SHEET 3 G 4 ALA B 221 ASN B 227 -1 N VAL B 226 O VAL B 243 SHEET 4 G 4 ILE B 188 ASN B 193 -1 N LYS B 189 O ALA B 225 SHEET 1 H 5 GLU B 271 PRO B 277 0 SHEET 2 H 5 ILE B 263 VAL B 268 -1 N LEU B 264 O MET B 276 SHEET 3 H 5 VAL B 253 ASP B 258 -1 N THR B 256 O THR B 265 SHEET 4 H 5 ILE B 374 VAL B 378 1 O GLU B 376 N ALA B 255 SHEET 5 H 5 GLY B 290 ILE B 293 -1 N TYR B 292 O VAL B 375 SHEET 1 I 4 ARG B 297 ASP B 304 0 SHEET 2 I 4 ARG B 319 GLN B 327 -1 O VAL B 322 N ILE B 301 SHEET 3 I 4 PHE B 334 SER B 337 -1 O VAL B 335 N THR B 326 SHEET 4 I 4 LEU B 355 VAL B 357 1 O LEU B 355 N PHE B 334 LINK C GLY A 353 N CSO A 354 1555 1555 1.35 LINK C CSO A 354 N LEU A 355 1555 1555 1.34 LINK C GLY B 353 N CSO B 354 1555 1555 1.34 LINK C CSO B 354 N LEU B 355 1555 1555 1.32 CISPEP 1 MET A 157 PRO A 158 0 -6.47 CISPEP 2 ASN A 193 PRO A 194 0 1.01 CISPEP 3 MET B 157 PRO B 158 0 4.28 CISPEP 4 MET B 157 PRO B 158 0 3.26 CISPEP 5 ASN B 193 PRO B 194 0 3.73 SITE 1 AC1 2 ASP A 323 HOH A 626 SITE 1 AC2 5 ASN B 242 GLN B 244 SER B 306 HOH B 647 SITE 2 AC2 5 HOH B 665 CRYST1 119.044 121.223 122.884 90.00 90.00 90.00 I 21 21 21 16 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 0.008400 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008249 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008138 0.00000