HEADER TRANSFERASE 29-JAN-13 4IZ9 TITLE CRYSTAL STRUCTURE OF AN ACETATE KINASE FROM MYCOBACTERIUM AVIUM BOUND TITLE 2 TO AN UNKNOWN ACID-APCPP CONJUGATE AND MANGANESE COMPND MOL_ID: 1; COMPND 2 MOLECULE: ACETATE KINASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: ACETOKINASE; COMPND 5 EC: 2.7.2.1; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MYCOBACTERIUM AVIUM; SOURCE 3 ORGANISM_TAXID: 243243; SOURCE 4 STRAIN: 104; SOURCE 5 GENE: ACKA; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PAVA0421 KEYWDS STRUCTURAL GENOMICS, SEATTLE STRUCTURAL GENOMICS CENTER FOR KEYWDS 2 INFECTIOUS DISEASE, SSGCID, ACKA, PROPIONATE KINASE, ACID-KINASE, KEYWDS 3 ATP-DEPENDENT, NON-HYDROLYZABLE ATP ANALOG, ANOMALOUS MANGANESE KEYWDS 4 SIGNAL, UNKNOWN CONJUGATE, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE (SSGCID) REVDAT 3 20-SEP-23 4IZ9 1 REMARK SEQADV LINK REVDAT 2 22-APR-15 4IZ9 1 JRNL REVDAT 1 20-FEB-13 4IZ9 0 JRNL AUTH L.BAUGH,I.PHAN,D.W.BEGLEY,M.C.CLIFTON,B.ARMOUR,D.M.DRANOW, JRNL AUTH 2 B.M.TAYLOR,M.M.MURUTHI,J.ABENDROTH,J.W.FAIRMAN,D.FOX, JRNL AUTH 3 S.H.DIETERICH,B.L.STAKER,A.S.GARDBERG,R.CHOI,S.N.HEWITT, JRNL AUTH 4 A.J.NAPULI,J.MYERS,L.K.BARRETT,Y.ZHANG,M.FERRELL,E.MUNDT, JRNL AUTH 5 K.THOMPKINS,N.TRAN,S.LYONS-ABBOTT,A.ABRAMOV,A.SEKAR, JRNL AUTH 6 D.SERBZHINSKIY,D.LORIMER,G.W.BUCHKO,R.STACY,L.J.STEWART, JRNL AUTH 7 T.E.EDWARDS,W.C.VAN VOORHIS,P.J.MYLER JRNL TITL INCREASING THE STRUCTURAL COVERAGE OF TUBERCULOSIS DRUG JRNL TITL 2 TARGETS. JRNL REF TUBERCULOSIS (EDINB) V. 95 142 2015 JRNL REFN ISSN 1472-9792 JRNL PMID 25613812 JRNL DOI 10.1016/J.TUBE.2014.12.003 REMARK 2 REMARK 2 RESOLUTION. 1.98 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) : 1.98 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.39 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 44007 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) : 0.174 REMARK 3 R VALUE (WORKING SET) : 0.173 REMARK 3 FREE R VALUE : 0.203 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2348 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) : 1.98 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.03 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3182 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.97 REMARK 3 BIN R VALUE (WORKING SET) : 0.2280 REMARK 3 BIN FREE R VALUE SET COUNT : 184 REMARK 3 BIN FREE R VALUE : 0.2650 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2830 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 55 REMARK 3 SOLVENT ATOMS : 300 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 34.16 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 39.28 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.37000 REMARK 3 B22 (A**2) : -0.37000 REMARK 3 B33 (A**2) : 0.73000 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): 0.114 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.112 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.072 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.950 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.962 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.948 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3051 ; 0.010 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 2907 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4165 ; 1.429 ; 1.999 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6653 ; 0.806 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 400 ; 5.981 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 131 ;31.664 ;22.061 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 464 ;13.728 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 35 ;19.830 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 473 ; 0.083 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3488 ; 0.006 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 705 ; 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): 1547 ; 1.624 ; 2.895 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1546 ; 1.624 ; 2.893 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1937 ; 2.464 ; 4.319 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 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 6 A 388 REMARK 3 ORIGIN FOR THE GROUP (A): 14.9578 39.5918 5.8384 REMARK 3 T TENSOR REMARK 3 T11: 0.0274 T22: 0.0083 REMARK 3 T33: 0.0501 T12: -0.0037 REMARK 3 T13: 0.0137 T23: -0.0049 REMARK 3 L TENSOR REMARK 3 L11: 0.3983 L22: 0.5074 REMARK 3 L33: 0.1289 L12: 0.0985 REMARK 3 L13: 0.0322 L23: 0.2544 REMARK 3 S TENSOR REMARK 3 S11: 0.0090 S12: 0.0134 S13: 0.1175 REMARK 3 S21: 0.0516 S22: -0.0520 S23: 0.1080 REMARK 3 S31: 0.0285 S32: -0.0232 S33: 0.0430 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: U VALUES WITH TLS ADDED. HYDROGENS HAVE REMARK 3 BEEN ADDED IN THE RIDING POSITIONS. REMARK 4 REMARK 4 4IZ9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 30-JAN-13. REMARK 100 THE DEPOSITION ID IS D_1000077396. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-OCT-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL 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 : RIGAKU FR-E+ SUPERBRIGHT REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : VARIMAX REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RIGAKU SATURN 944+ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 44007 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.980 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 10.20 REMARK 200 R MERGE (I) : 0.11600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.9200 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.98 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.26 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.52400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 6.340 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: PDB ENTRY 3P4I REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 68.36 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.89 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: MYAVA.00640.A.A1 PS00663 AT 20 MG/ML REMARK 280 WITH 2 MM APCPP AND 2 MM MNCL2 AGAINST PACT SCREEN CONDITION A4, REMARK 280 0.1 M SPG BUFFER PH 7.0, 25% PEG 3350 AND 15% ETHYLENE GLYCOL AS REMARK 280 CRYO-PROTECTANT, CRYSTAL TRACKING ID 236958A4, UNIQUE PUCK ID REMARK 280 LQA0-2, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 289K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 70.61500 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 47.88500 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 47.88500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 35.30750 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 47.88500 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 47.88500 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 105.92250 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 47.88500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 47.88500 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 35.30750 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 47.88500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 47.88500 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 105.92250 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 70.61500 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 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 10280 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 27390 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -19.0 KCAL/MOL 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 BIOMT1 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 707 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 708 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 754 LIES ON A SPECIAL POSITION. 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 -3 REMARK 465 PRO A -2 REMARK 465 GLY A -1 REMARK 465 SER A 0 REMARK 465 MET A 1 REMARK 465 VAL A 2 REMARK 465 ASP A 3 REMARK 465 GLY A 4 REMARK 465 SER A 5 REMARK 465 GLU A 45 REMARK 465 SER A 46 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 ASP A 6 CG OD1 OD2 REMARK 470 VAL A 32 CG1 CG2 REMARK 470 ARG A 41 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 57 CG CD NE CZ NH1 NH2 REMARK 470 ASP A 69 CG OD1 OD2 REMARK 470 THR A 72 OG1 CG2 REMARK 470 ARG A 190 CG CD NE CZ NH1 NH2 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 O4 SIN A 403 O HOH A 639 1.93 REMARK 500 O3G APC A 402 O HOH A 638 2.12 REMARK 500 O HOH A 699 O HOH A 700 2.17 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 144 34.59 -99.87 REMARK 500 SER A 262 -155.13 -126.13 REMARK 500 ALA A 319 -173.17 69.20 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 MN A 401 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 374 OE1 REMARK 620 2 APC A 402 O1B 163.5 REMARK 620 3 APC A 402 O1B 156.4 32.7 REMARK 620 4 SIN A 403 O4 132.6 31.8 53.0 REMARK 620 5 SIN A 403 O4 106.9 56.6 80.5 27.6 REMARK 620 6 HOH A 638 O 93.2 90.3 107.0 107.6 104.0 REMARK 620 7 HOH A 639 O 81.2 84.4 115.9 65.8 41.8 73.1 REMARK 620 N 1 2 3 4 5 6 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE APC A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SIN A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 405 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 406 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 407 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3P4I RELATED DB: PDB REMARK 900 APO STRUCTURE REMARK 900 RELATED ID: 4DQ8 RELATED DB: PDB REMARK 900 APO ACKA FROM MYCOBACTERIUM MARINUM REMARK 900 RELATED ID: 3R9P RELATED DB: PDB REMARK 900 APO ACKA FROM MYCOBACTERIUM PARATUBERCULOSIS REMARK 900 RELATED ID: 4IJN RELATED DB: PDB REMARK 900 ACKA FROM MYCOBACTERIUM SMEGMATIS BOUND TO AMP AND SULFATE REMARK 900 RELATED ID: MYAVA.00640.A RELATED DB: TARGETTRACK DBREF 4IZ9 A 3 388 UNP A0QLU8 A0QLU8_MYCA1 2 387 SEQADV 4IZ9 GLY A -3 UNP A0QLU8 EXPRESSION TAG SEQADV 4IZ9 PRO A -2 UNP A0QLU8 EXPRESSION TAG SEQADV 4IZ9 GLY A -1 UNP A0QLU8 EXPRESSION TAG SEQADV 4IZ9 SER A 0 UNP A0QLU8 EXPRESSION TAG SEQADV 4IZ9 MET A 1 UNP A0QLU8 EXPRESSION TAG SEQADV 4IZ9 VAL A 2 UNP A0QLU8 EXPRESSION TAG SEQRES 1 A 392 GLY PRO GLY SER MET VAL ASP GLY SER ASP GLY ALA ARG SEQRES 2 A 392 ARG VAL LEU VAL ILE ASN SER GLY SER SER SER LEU LYS SEQRES 3 A 392 PHE GLN LEU VAL ASP PRO GLU SER GLY VAL ALA ALA SER SEQRES 4 A 392 THR GLY ILE VAL GLU ARG ILE GLY GLU GLU SER SER PRO SEQRES 5 A 392 VAL PRO ASP HIS ASP ALA ALA LEU ARG ARG ALA PHE ASP SEQRES 6 A 392 MET LEU ALA GLY ASP GLY VAL ASP LEU ASN THR ALA GLY SEQRES 7 A 392 LEU VAL ALA VAL GLY HIS ARG VAL VAL HIS GLY GLY ASN SEQRES 8 A 392 THR PHE TYR ARG PRO THR VAL LEU ASP ASP ALA VAL ILE SEQRES 9 A 392 ALA ARG LEU HIS GLU LEU SER GLU LEU ALA PRO LEU HIS SEQRES 10 A 392 ASN PRO PRO ALA LEU LEU GLY ILE GLU VAL ALA ARG ARG SEQRES 11 A 392 LEU LEU PRO GLY ILE ALA HIS VAL ALA VAL PHE ASP THR SEQRES 12 A 392 GLY PHE PHE HIS ASP LEU PRO PRO ALA ALA ALA THR TYR SEQRES 13 A 392 ALA ILE ASP ARG GLU LEU ALA ASP ARG TRP GLN ILE ARG SEQRES 14 A 392 ARG TYR GLY PHE HIS GLY THR SER HIS ARG TYR VAL SER SEQRES 15 A 392 GLU GLN ALA ALA ALA PHE LEU ASP ARG PRO LEU ARG GLY SEQRES 16 A 392 LEU LYS GLN ILE VAL LEU HIS LEU GLY ASN GLY CYS SER SEQRES 17 A 392 ALA SER ALA ILE ALA GLY THR ARG PRO LEU ASP THR SER SEQRES 18 A 392 MET GLY LEU THR PRO LEU GLU GLY LEU VAL MET GLY THR SEQRES 19 A 392 ARG SER GLY ASP ILE ASP PRO SER VAL VAL SER TYR LEU SEQRES 20 A 392 CYS HIS THR ALA GLY MET GLY VAL ASP ASP VAL GLU SER SEQRES 21 A 392 MET LEU ASN HIS ARG SER GLY VAL VAL GLY LEU SER GLY SEQRES 22 A 392 VAL ARG ASP PHE ARG ARG LEU ARG GLU LEU ILE GLU SER SEQRES 23 A 392 GLY ASP GLY ALA ALA GLN LEU ALA TYR SER VAL PHE THR SEQRES 24 A 392 HIS ARG LEU ARG LYS TYR ILE GLY ALA TYR LEU ALA VAL SEQRES 25 A 392 LEU GLY HIS THR ASP VAL ILE SER PHE THR ALA GLY ILE SEQRES 26 A 392 GLY GLU ASN ASP ALA ALA VAL ARG ARG ASP ALA VAL SER SEQRES 27 A 392 GLY MET GLU GLU LEU GLY ILE VAL LEU ASP GLU ARG ARG SEQRES 28 A 392 ASN LEU PRO GLY ALA LYS GLY ALA ARG GLN ILE SER ALA SEQRES 29 A 392 ASP ASP SER PRO ILE THR VAL LEU VAL VAL PRO THR ASN SEQRES 30 A 392 GLU GLU LEU ALA ILE ALA ARG ASP CYS VAL ARG VAL LEU SEQRES 31 A 392 GLY GLY HET MN A 401 1 HET APC A 402 60 HET SIN A 403 16 HET EDO A 404 4 HET EDO A 405 4 HET EDO A 406 4 HET EDO A 407 4 HETNAM MN MANGANESE (II) ION HETNAM APC DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER HETNAM SIN SUCCINIC ACID HETNAM EDO 1,2-ETHANEDIOL HETSYN APC ALPHA,BETA-METHYLENEADENOSINE-5'-TRIPHOSPHATE HETSYN EDO ETHYLENE GLYCOL FORMUL 2 MN MN 2+ FORMUL 3 APC C11 H18 N5 O12 P3 FORMUL 4 SIN C4 H6 O4 FORMUL 5 EDO 4(C2 H6 O2) FORMUL 9 HOH *300(H2 O) HELIX 1 1 ASP A 51 ASP A 66 1 16 HELIX 2 2 ASP A 96 GLU A 105 1 10 HELIX 3 3 HIS A 113 LEU A 128 1 16 HELIX 4 4 THR A 139 HIS A 143 5 5 HELIX 5 5 PRO A 146 THR A 151 1 6 HELIX 6 6 ASP A 155 GLN A 163 1 9 HELIX 7 7 HIS A 170 ASP A 186 1 17 HELIX 8 8 PRO A 188 GLY A 191 5 4 HELIX 9 9 PRO A 237 ALA A 247 1 11 HELIX 10 10 GLY A 250 ARG A 261 1 12 HELIX 11 11 SER A 262 GLY A 269 1 8 HELIX 12 12 ASP A 272 SER A 282 1 11 HELIX 13 13 ASP A 284 GLY A 310 1 27 HELIX 14 14 ALA A 319 ASP A 325 1 7 HELIX 15 15 ASP A 325 SER A 334 1 10 HELIX 16 16 MET A 336 GLY A 340 5 5 HELIX 17 17 ASN A 373 LEU A 386 1 14 SHEET 1 A 6 ALA A 33 VAL A 39 0 SHEET 2 A 6 LEU A 21 VAL A 26 -1 N LEU A 25 O SER A 35 SHEET 3 A 6 ARG A 10 SER A 16 -1 N VAL A 13 O GLN A 24 SHEET 4 A 6 LEU A 75 VAL A 82 1 O GLY A 79 N ILE A 14 SHEET 5 A 6 ALA A 132 PHE A 137 1 O VAL A 134 N HIS A 80 SHEET 6 A 6 THR A 93 VAL A 94 -1 N THR A 93 O ALA A 135 SHEET 1 B 6 ARG A 212 THR A 216 0 SHEET 2 B 6 CYS A 203 ALA A 209 -1 N ALA A 207 O LEU A 214 SHEET 3 B 6 LYS A 193 LEU A 199 -1 N GLN A 194 O ILE A 208 SHEET 4 B 6 VAL A 314 THR A 318 1 O SER A 316 N LEU A 197 SHEET 5 B 6 THR A 366 VAL A 369 1 O LEU A 368 N ILE A 315 SHEET 6 B 6 ARG A 356 GLN A 357 -1 N ARG A 356 O VAL A 369 LINK PG AAPC A 402 O2 ASIN A 403 1555 1555 1.59 LINK PG BAPC A 402 O2 BSIN A 403 1555 1555 1.62 LINK OE1 GLU A 374 MN MN A 401 1555 1555 2.47 LINK MN MN A 401 O1BAAPC A 402 1555 1555 2.19 LINK MN MN A 401 O1BBAPC A 402 1555 1555 2.39 LINK MN MN A 401 O4 BSIN A 403 1555 1555 2.71 LINK MN MN A 401 O4 ASIN A 403 1555 1555 2.77 LINK MN MN A 401 O HOH A 638 1555 1555 1.82 LINK MN MN A 401 O HOH A 639 1555 1555 2.62 SITE 1 AC1 6 GLU A 374 APC A 402 SIN A 403 HOH A 637 SITE 2 AC1 6 HOH A 638 HOH A 639 SITE 1 AC2 21 ASN A 15 LYS A 22 GLU A 105 GLY A 200 SITE 2 AC2 21 ASN A 201 ASP A 272 PHE A 273 ARG A 274 SITE 3 AC2 21 ALA A 319 GLY A 320 ILE A 321 ASN A 324 SITE 4 AC2 21 ASP A 325 MN A 401 SIN A 403 HOH A 578 SITE 5 AC2 21 HOH A 634 HOH A 637 HOH A 638 HOH A 722 SITE 6 AC2 21 HOH A 781 SITE 1 AC3 10 ARG A 81 HIS A 170 HIS A 198 GLY A 200 SITE 2 AC3 10 ASN A 201 GLY A 202 MN A 401 APC A 402 SITE 3 AC3 10 EDO A 404 HOH A 639 SITE 1 AC4 7 ARG A 81 ASP A 138 HIS A 170 MET A 218 SITE 2 AC4 7 PRO A 222 ARG A 231 SIN A 403 SITE 1 AC5 3 ALA A 150 THR A 151 HOH A 648 SITE 1 AC6 5 GLN A 288 SER A 292 THR A 295 HOH A 533 SITE 2 AC6 5 HOH A 705 SITE 1 AC7 6 LEU A 306 GLY A 310 HIS A 311 THR A 312 SITE 2 AC7 6 GLU A 338 HOH A 709 CRYST1 95.770 95.770 141.230 90.00 90.00 90.00 P 41 21 2 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 0.010442 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010442 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007081 0.00000