HEADER TRANSFERASE 05-NOV-08 3F61 TITLE CRYSTAL STRUCTURE OF M. TUBERCULOSIS PKNB LEU33ASP/VAL222ASP DOUBLE TITLE 2 MUTANT IN COMPLEX WITH ADP COMPND MOL_ID: 1; COMPND 2 MOLECULE: SERINE/THREONINE-PROTEIN KINASE PKNB; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: PKNB KINASE DOMAIN; COMPND 5 EC: 2.7.11.1; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MYCOBACTERIUM TUBERCULOSIS; SOURCE 3 ORGANISM_TAXID: 1773; SOURCE 4 STRAIN: H37RV; SOURCE 5 GENE: MT0017, MTCY10H4.14C, PKNB, RV0014C; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21-CODON PLUS; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET28B KEYWDS PROTEIN KINASE, PKNB, MYCOBACTERIUM TUBERCULOSIS, STRUCTURAL KEYWDS 2 GENOMICS, PKNB KD DOUBLE MUTANT BOUND TO ADP, TB STRUCTURAL GENOMICS KEYWDS 3 CONSORTIUM, TBSGC, ATP-BINDING, KINASE, MAGNESIUM, METAL-BINDING, KEYWDS 4 NUCLEOTIDE-BINDING, PHOSPHOPROTEIN, SERINE/THREONINE-PROTEIN KINASE, KEYWDS 5 TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR C.A.MIECZKOWSKI,T.ALBER,TB STRUCTURAL GENOMICS CONSORTIUM (TBSGC) REVDAT 7 03-APR-24 3F61 1 REMARK REVDAT 6 27-DEC-23 3F61 1 REMARK REVDAT 5 20-OCT-21 3F61 1 REMARK SEQADV LINK REVDAT 4 24-JAN-18 3F61 1 AUTHOR REVDAT 3 25-OCT-17 3F61 1 REMARK REVDAT 2 13-JAN-09 3F61 1 JRNL REVDAT 1 02-DEC-08 3F61 0 JRNL AUTH C.MIECZKOWSKI,A.T.IAVARONE,T.ALBER JRNL TITL AUTO-ACTIVATION MECHANISM OF THE MYCOBACTERIUM TUBERCULOSIS JRNL TITL 2 PKNB RECEPTOR SER/THR KINASE. JRNL REF EMBO J. V. 27 3186 2008 JRNL REFN ISSN 0261-4189 JRNL PMID 19008858 JRNL DOI 10.1038/EMBOJ.2008.236 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.77 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 27635 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) : 0.205 REMARK 3 R VALUE (WORKING SET) : 0.203 REMARK 3 FREE R VALUE : 0.228 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1477 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) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.85 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1901 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 93.88 REMARK 3 BIN R VALUE (WORKING SET) : 0.3100 REMARK 3 BIN FREE R VALUE SET COUNT : 107 REMARK 3 BIN FREE R VALUE : 0.3080 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2083 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 31 REMARK 3 SOLVENT ATOMS : 184 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.62 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.01000 REMARK 3 B22 (A**2) : 0.00000 REMARK 3 B33 (A**2) : 0.00000 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): 0.133 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.122 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.084 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.750 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.958 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.945 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2192 ; 0.012 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3007 ; 1.461 ; 1.983 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 285 ; 5.547 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 99 ;31.002 ;23.535 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 335 ;14.316 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 19 ;20.414 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 341 ; 0.095 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1708 ; 0.007 ; 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): 1393 ; 0.877 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2259 ; 1.554 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 799 ; 2.253 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 744 ; 3.764 ; 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 : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS REMARK 3 U VALUES : REFINED INDIVIDUALLY REMARK 4 REMARK 4 3F61 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-NOV-08. REMARK 100 THE DEPOSITION ID IS D_1000050190. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-MAR-07 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 8.3.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.11586 REMARK 200 MONOCHROMATOR : SI 111 CHANNEL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 29112 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 200 DATA REDUNDANCY : 8.000 REMARK 200 R MERGE (I) : 0.05600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 48.6070 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.86 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.4 REMARK 200 DATA REDUNDANCY IN SHELL : 6.40 REMARK 200 R MERGE FOR SHELL (I) : 0.36000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.760 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: PKNB LEU33ASP IN COMPLEX WITH ATPGS REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.96 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.28 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG 3000, 3 MM ADP, 0.2 M NAF, REMARK 280 100MM TRIS PH 8.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 277K 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 19.49050 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 76.21700 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 25.77100 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 76.21700 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 19.49050 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 25.77100 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 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 GLY A -2 REMARK 465 SER A -1 REMARK 465 HIS A 0 REMARK 465 ARG A 161 REMARK 465 ALA A 162 REMARK 465 ILE A 163 REMARK 465 ALA A 164 REMARK 465 ASP A 165 REMARK 465 SER A 166 REMARK 465 GLY A 167 REMARK 465 ASN A 168 REMARK 465 SER A 169 REMARK 465 VAL A 170 REMARK 465 THR A 171 REMARK 465 GLN A 172 REMARK 465 THR A 173 REMARK 465 ALA A 174 REMARK 465 ALA A 175 REMARK 465 VAL A 176 REMARK 465 ILE A 177 REMARK 465 GLY A 178 REMARK 465 THR A 179 REMARK 465 ALA A 291 REMARK 465 GLU A 292 REMARK 465 ARG A 293 REMARK 465 THR A 294 REMARK 465 SER A 295 REMARK 465 LEU A 296 REMARK 465 LEU A 297 REMARK 465 SER A 298 REMARK 465 SER A 299 REMARK 465 ALA A 300 REMARK 465 ALA A 301 REMARK 465 GLY A 302 REMARK 465 ASN A 303 REMARK 465 LEU A 304 REMARK 465 SER A 305 REMARK 465 GLY A 306 REMARK 465 PRO A 307 REMARK 465 ARG A 308 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 MET A 1 CG SD CE REMARK 480 ARG A 48 NE CZ NH1 NH2 REMARK 480 GLU A 107 CD OE1 OE2 REMARK 480 LYS A 113 CD CE NZ REMARK 480 ASP A 222 OD1 OD2 REMARK 480 GLU A 260 CD OE1 OE2 REMARK 480 LYS A 286 CE NZ REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 ARG A 48 CD ARG A 48 NE -0.235 REMARK 500 GLU A 107 CG GLU A 107 CD -0.151 REMARK 500 GLU A 260 CG GLU A 260 CD -0.098 REMARK 500 REMARK 500 REMARK: NULL 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 ARG A 48 CG - CD - NE ANGL. DEV. = 20.7 DEGREES REMARK 500 ARG A 48 CD - NE - CZ ANGL. DEV. = 29.2 DEGREES REMARK 500 ARG A 196 NE - CZ - NH2 ANGL. DEV. = -4.9 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 ASP A 9 18.19 49.15 REMARK 500 ARG A 10 -38.79 -130.52 REMARK 500 ARG A 137 -14.45 82.27 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 310 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN A 143 OD1 REMARK 620 2 ASP A 156 OD2 91.0 REMARK 620 3 ADP A 340 O1B 90.8 178.2 REMARK 620 4 ADP A 340 O2A 178.9 87.9 90.3 REMARK 620 5 HOH A 410 O 83.0 91.1 88.6 97.0 REMARK 620 6 HOH A 411 O 87.1 91.0 89.6 93.0 169.9 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ADP A 340 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 310 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 311 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 312 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 313 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: RV0014C RELATED DB: TARGETDB DBREF 3F61 A 1 308 UNP P0A5S4 PKNB_MYCTU 1 308 SEQADV 3F61 GLY A -2 UNP P0A5S4 EXPRESSION TAG SEQADV 3F61 SER A -1 UNP P0A5S4 EXPRESSION TAG SEQADV 3F61 HIS A 0 UNP P0A5S4 EXPRESSION TAG SEQADV 3F61 ASP A 33 UNP P0A5S4 LEU 33 ENGINEERED MUTATION SEQADV 3F61 ASP A 222 UNP P0A5S4 VAL 222 ENGINEERED MUTATION SEQRES 1 A 311 GLY SER HIS MET THR THR PRO SER HIS LEU SER ASP ARG SEQRES 2 A 311 TYR GLU LEU GLY GLU ILE LEU GLY PHE GLY GLY MET SER SEQRES 3 A 311 GLU VAL HIS LEU ALA ARG ASP LEU ARG ASP HIS ARG ASP SEQRES 4 A 311 VAL ALA VAL LYS VAL LEU ARG ALA ASP LEU ALA ARG ASP SEQRES 5 A 311 PRO SER PHE TYR LEU ARG PHE ARG ARG GLU ALA GLN ASN SEQRES 6 A 311 ALA ALA ALA LEU ASN HIS PRO ALA ILE VAL ALA VAL TYR SEQRES 7 A 311 ASP THR GLY GLU ALA GLU THR PRO ALA GLY PRO LEU PRO SEQRES 8 A 311 TYR ILE VAL MET GLU TYR VAL ASP GLY VAL THR LEU ARG SEQRES 9 A 311 ASP ILE VAL HIS THR GLU GLY PRO MET THR PRO LYS ARG SEQRES 10 A 311 ALA ILE GLU VAL ILE ALA ASP ALA CYS GLN ALA LEU ASN SEQRES 11 A 311 PHE SER HIS GLN ASN GLY ILE ILE HIS ARG ASP VAL LYS SEQRES 12 A 311 PRO ALA ASN ILE MET ILE SER ALA THR ASN ALA VAL LYS SEQRES 13 A 311 VAL MET ASP PHE GLY ILE ALA ARG ALA ILE ALA ASP SER SEQRES 14 A 311 GLY ASN SER VAL THR GLN THR ALA ALA VAL ILE GLY THR SEQRES 15 A 311 ALA GLN TYR LEU SER PRO GLU GLN ALA ARG GLY ASP SER SEQRES 16 A 311 VAL ASP ALA ARG SER ASP VAL TYR SER LEU GLY CYS VAL SEQRES 17 A 311 LEU TYR GLU VAL LEU THR GLY GLU PRO PRO PHE THR GLY SEQRES 18 A 311 ASP SER PRO ASP SER VAL ALA TYR GLN HIS VAL ARG GLU SEQRES 19 A 311 ASP PRO ILE PRO PRO SER ALA ARG HIS GLU GLY LEU SER SEQRES 20 A 311 ALA ASP LEU ASP ALA VAL VAL LEU LYS ALA LEU ALA LYS SEQRES 21 A 311 ASN PRO GLU ASN ARG TYR GLN THR ALA ALA GLU MET ARG SEQRES 22 A 311 ALA ASP LEU VAL ARG VAL HIS ASN GLY GLU PRO PRO GLU SEQRES 23 A 311 ALA PRO LYS VAL LEU THR ASP ALA GLU ARG THR SER LEU SEQRES 24 A 311 LEU SER SER ALA ALA GLY ASN LEU SER GLY PRO ARG HET ADP A 340 27 HET MG A 310 1 HET MG A 311 1 HET MG A 312 1 HET MG A 313 1 HETNAM ADP ADENOSINE-5'-DIPHOSPHATE HETNAM MG MAGNESIUM ION FORMUL 2 ADP C10 H15 N5 O10 P2 FORMUL 3 MG 4(MG 2+) FORMUL 7 HOH *184(H2 O) HELIX 1 1 ALA A 44 ALA A 47 5 4 HELIX 2 2 ASP A 49 GLN A 61 1 13 HELIX 3 3 LEU A 100 GLY A 108 1 9 HELIX 4 4 THR A 111 ASN A 132 1 22 HELIX 5 5 LYS A 140 ALA A 142 5 3 HELIX 6 6 SER A 184 GLY A 190 1 7 HELIX 7 7 ASP A 194 GLY A 212 1 19 HELIX 8 8 SER A 220 GLU A 231 1 12 HELIX 9 9 PRO A 235 HIS A 240 1 6 HELIX 10 10 SER A 244 LEU A 255 1 12 HELIX 11 11 ASN A 258 ARG A 262 5 5 HELIX 12 12 THR A 265 ASN A 278 1 14 SHEET 1 A 6 HIS A 6 LEU A 7 0 SHEET 2 A 6 TYR A 11 PHE A 19 -1 O TYR A 11 N LEU A 7 SHEET 3 A 6 SER A 23 ASP A 30 -1 O LEU A 27 N GLY A 14 SHEET 4 A 6 ARG A 35 LEU A 42 -1 O ARG A 35 N ASP A 30 SHEET 5 A 6 GLY A 85 GLU A 93 -1 O ILE A 90 N LYS A 40 SHEET 6 A 6 VAL A 74 THR A 82 -1 N ASP A 76 O VAL A 91 SHEET 1 B 3 GLY A 97 THR A 99 0 SHEET 2 B 3 ILE A 144 SER A 147 -1 O ILE A 146 N VAL A 98 SHEET 3 B 3 VAL A 152 VAL A 154 -1 O LYS A 153 N MET A 145 LINK OD1 ASN A 143 MG MG A 310 1555 1555 2.11 LINK OD2 ASP A 156 MG MG A 310 1555 1555 2.02 LINK MG MG A 310 O1B ADP A 340 1555 1555 2.14 LINK MG MG A 310 O2A ADP A 340 1555 1555 2.01 LINK MG MG A 310 O HOH A 410 1555 1555 2.19 LINK MG MG A 310 O HOH A 411 1555 1555 2.09 SITE 1 AC1 26 GLY A 18 PHE A 19 SER A 23 VAL A 25 SITE 2 AC1 26 LYS A 40 MET A 92 GLU A 93 VAL A 95 SITE 3 AC1 26 THR A 99 LYS A 140 ALA A 142 ASN A 143 SITE 4 AC1 26 MET A 145 MET A 155 ASP A 156 MG A 310 SITE 5 AC1 26 MG A 312 HOH A 315 HOH A 358 HOH A 386 SITE 6 AC1 26 HOH A 394 HOH A 404 HOH A 409 HOH A 410 SITE 7 AC1 26 HOH A 411 HOH A 453 SITE 1 AC2 5 ASN A 143 ASP A 156 ADP A 340 HOH A 410 SITE 2 AC2 5 HOH A 411 SITE 1 AC3 4 PRO A 141 ALA A 142 HOH A 385 HOH A 404 SITE 1 AC4 6 GLY A 20 GLY A 21 MET A 22 SER A 23 SITE 2 AC4 6 ADP A 340 HOH A 394 SITE 1 AC5 2 ASN A 127 ALA A 267 CRYST1 38.981 51.542 152.434 90.00 90.00 90.00 P 21 21 21 4 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 0.025654 0.000000 0.000000 0.00000 SCALE2 0.000000 0.019402 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006560 0.00000