PDB Short entry for 3I73 HEADER HYDROLASE 08-JUL-09 3I73 TITLE STRUCTURAL CHARACTERIZATION FOR THE NUCLEOTIDE BINDING ABILITY OF TITLE 2 SUBUNIT A WITH ADP OF THE A1AO ATP SYNTHASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: A-TYPE ATP SYNTHASE CATALYTIC SUBUNIT A; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 1-240, 617-964; COMPND 5 SYNONYM: V-TYPE ATP SYNTHASE ALPHA CHAIN, V-ATPASE SUBUNIT A; COMPND 6 EC: 3.6.3.14; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PYROCOCCUS HORIKOSHII; SOURCE 3 ORGANISM_TAXID: 70601; SOURCE 4 STRAIN: OT3; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21 DE3 RIL; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET22B(+)-HIS6 KEYWDS HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR S.M.S.MANIMEKALAI,A.KUMAR,A.M.BALAKRISHNA,G.GRUBER REVDAT 5 10-NOV-21 3I73 1 REMARK SEQADV REVDAT 4 01-NOV-17 3I73 1 REMARK REVDAT 3 23-AUG-17 3I73 1 SOURCE REMARK REVDAT 2 13-NOV-13 3I73 1 JRNL VERSN REVDAT 1 12-JAN-10 3I73 0 JRNL AUTH A.KUMAR,M.S.MANIMEKALAI,A.M.BALAKRISHNA,J.JEYAKANTHAN, JRNL AUTH 2 G.GRUBER JRNL TITL NUCLEOTIDE BINDING STATES OF SUBUNIT A OF THE A-ATP SYNTHASE JRNL TITL 2 AND THE IMPLICATION OF P-LOOP SWITCH IN EVOLUTION. JRNL REF J.MOL.BIOL. V. 396 301 2010 JRNL REFN ISSN 0022-2836 JRNL PMID 19944110 JRNL DOI 10.1016/J.JMB.2009.11.046 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH Y.MAEGAWA,H.MORITA,D.IYAGUCHI,M.YAO,N.WATANABE,I.TANAKA REMARK 1 TITL STRUCTURE OF THE CATALYTIC NUCLEOTIDE-BINDING SUBUNIT A OF REMARK 1 TITL 2 A-TYPE ATP SYNTHASE FROM PYROCOCCUS HORIKOSHII REVEALS A REMARK 1 TITL 3 NOVEL DOMAIN RELATED TO THE PERIPHERAL STALK. REMARK 1 REF ACTA CRYSTALLOGR.,SECT.D V. 62 483 2006 REMARK 1 REFN ISSN 0907-4449 REMARK 1 PMID 16627940 REMARK 1 DOI 10.1107/S0907444906006329 REMARK 2 REMARK 2 RESOLUTION. 2.40 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) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.72 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 34683 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) : 0.227 REMARK 3 R VALUE (WORKING SET) : 0.225 REMARK 3 FREE R VALUE : 0.258 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1729 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) : 2.40 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.47 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2392 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.2660 REMARK 3 BIN FREE R VALUE SET COUNT : 120 REMARK 3 BIN FREE R VALUE : 0.3390 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4050 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 63 REMARK 3 SOLVENT ATOMS : 295 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 56.30 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 57.50 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.00000 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): 0.296 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.231 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.145 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 6.046 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.932 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.914 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4199 ; 0.013 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5696 ; 1.623 ; 1.994 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 510 ; 9.005 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 180 ;35.645 ;23.667 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 736 ;17.898 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 33 ;21.067 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 628 ; 0.108 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3128 ; 0.012 ; 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): 2562 ; 0.889 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4157 ; 1.661 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1637 ; 2.124 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1539 ; 3.692 ; 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 3I73 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 16-JUL-09. REMARK 100 THE DEPOSITION ID IS D_1000054046. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-NOV-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSRRC REMARK 200 BEAMLINE : BL13B1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 34741 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 8.600 REMARK 200 R MERGE (I) : 0.05100 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 53.1900 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.49 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 8.90 REMARK 200 R MERGE FOR SHELL (I) : 0.45700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 5.130 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: PDB ENTRY 1VDZ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 62.65 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.29 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 50% (V/V) MPD, 0.1 M ACETATE (PH 4.5), REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 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+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 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 52.49550 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 64.23600 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 64.23600 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 78.74325 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 64.23600 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 64.23600 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 26.24775 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 64.23600 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 64.23600 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 78.74325 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 64.23600 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 64.23600 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 26.24775 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 52.49550 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: MONOMERIC 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 MET A 1 REMARK 465 VAL A 2 REMARK 465 ALA A 3 REMARK 465 LYS A 4 REMARK 465 GLY A 5 REMARK 465 ARG A 6 REMARK 465 ILE A 7 REMARK 465 ILE A 8 REMARK 465 ARG A 9 REMARK 465 VAL A 10 REMARK 465 THR A 11 REMARK 465 GLY A 12 REMARK 465 PRO A 13 REMARK 465 LEU A 14 REMARK 465 VAL A 15 REMARK 465 VAL A 16 REMARK 465 ALA A 17 REMARK 465 ASP A 18 REMARK 465 GLY A 19 REMARK 465 MET A 20 REMARK 465 LYS A 21 REMARK 465 GLY A 22 REMARK 465 ALA A 23 REMARK 465 LYS A 24 REMARK 465 MET A 25 REMARK 465 TYR A 26 REMARK 465 GLU A 27 REMARK 465 VAL A 28 REMARK 465 VAL A 29 REMARK 465 ARG A 30 REMARK 465 VAL A 31 REMARK 465 GLY A 32 REMARK 465 GLU A 33 REMARK 465 LEU A 34 REMARK 465 GLY A 35 REMARK 465 LEU A 36 REMARK 465 ILE A 37 REMARK 465 GLY A 38 REMARK 465 GLU A 39 REMARK 465 ILE A 40 REMARK 465 ILE A 41 REMARK 465 ARG A 42 REMARK 465 LEU A 43 REMARK 465 GLU A 44 REMARK 465 GLY A 45 REMARK 465 ASP A 46 REMARK 465 LYS A 47 REMARK 465 ALA A 48 REMARK 465 VAL A 49 REMARK 465 ILE A 50 REMARK 465 GLN A 51 REMARK 465 VAL A 52 REMARK 465 TYR A 53 REMARK 465 GLU A 54 REMARK 465 GLU A 55 REMARK 465 THR A 56 REMARK 465 ALA A 57 REMARK 465 GLY A 58 REMARK 465 VAL A 59 REMARK 465 ARG A 60 REMARK 465 PRO A 61 REMARK 465 GLY A 62 REMARK 465 LEU A 340 REMARK 465 ARG A 341 REMARK 465 GLU A 342 REMARK 465 ILE A 343 REMARK 465 SER A 344 REMARK 465 GLY A 345 REMARK 465 ARG A 346 REMARK 465 LEU A 347 REMARK 465 GLU A 348 REMARK 465 GLU A 349 REMARK 465 MET A 350 REMARK 465 PRO A 351 REMARK 465 GLY A 352 REMARK 465 GLU A 353 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 PRO A 235 C - N - CA ANGL. DEV. = 11.5 DEGREES REMARK 500 PRO A 235 C - N - CD ANGL. DEV. = -23.0 DEGREES REMARK 500 PRO A 428 C - N - CD ANGL. DEV. = -21.7 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 65 160.96 162.47 REMARK 500 THR A 68 60.03 -111.21 REMARK 500 ALA A 70 69.14 78.70 REMARK 500 ARG A 79 13.36 94.73 REMARK 500 THR A 82 -5.61 76.47 REMARK 500 LEU A 92 83.57 -5.66 REMARK 500 GLU A 93 105.65 51.91 REMARK 500 VAL A 94 -134.43 -111.70 REMARK 500 ILE A 95 -132.13 -131.12 REMARK 500 THR A 99 -124.00 68.90 REMARK 500 ASP A 101 -19.35 67.01 REMARK 500 PHE A 102 -71.94 -139.02 REMARK 500 ALA A 109 138.93 171.88 REMARK 500 PRO A 140 99.58 -66.61 REMARK 500 GLU A 208 -38.24 -153.88 REMARK 500 PRO A 235 98.34 46.18 REMARK 500 ILE A 259 79.62 -104.65 REMARK 500 MET A 268 -42.95 -162.38 REMARK 500 GLU A 289 1.53 -67.97 REMARK 500 ARG A 290 20.76 -143.87 REMARK 500 SER A 334 99.19 -58.29 REMARK 500 TYR A 356 -152.43 -65.81 REMARK 500 PRO A 357 -61.93 21.52 REMARK 500 PHE A 399 59.82 -91.89 REMARK 500 SER A 400 -100.18 -104.89 REMARK 500 GLU A 401 -149.41 -78.58 REMARK 500 PRO A 402 -123.24 14.77 REMARK 500 PRO A 428 123.30 -5.18 REMARK 500 ALA A 429 45.45 -81.52 REMARK 500 ILE A 451 -57.63 -120.11 REMARK 500 TYR A 502 -59.13 -125.09 REMARK 500 ASN A 539 -1.16 -59.12 REMARK 500 LYS A 585 -16.43 -49.82 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 GLY A 234 PRO A 235 -124.97 REMARK 500 TYR A 356 PRO A 357 -143.62 REMARK 500 GLU A 401 PRO A 402 -140.04 REMARK 500 PHE A 427 PRO A 428 -66.22 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 PHE A 427 -11.73 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 ADP A 589 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MPD A 590 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MPD A 591 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MPD A 592 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE TRS A 593 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACY A 594 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3I72 RELATED DB: PDB REMARK 900 RELATED ID: 3I4L RELATED DB: PDB REMARK 900 RELATED ID: 1VDZ RELATED DB: PDB DBREF 3I73 A 1 240 UNP O57728 VATA_PYRHO 1 240 DBREF 3I73 A 241 588 UNP O57728 VATA_PYRHO 617 964 SEQADV 3I73 ARG A 79 UNP O57728 GLY 79 ENGINEERED MUTATION SEQRES 1 A 588 MET VAL ALA LYS GLY ARG ILE ILE ARG VAL THR GLY PRO SEQRES 2 A 588 LEU VAL VAL ALA ASP GLY MET LYS GLY ALA LYS MET TYR SEQRES 3 A 588 GLU VAL VAL ARG VAL GLY GLU LEU GLY LEU ILE GLY GLU SEQRES 4 A 588 ILE ILE ARG LEU GLU GLY ASP LYS ALA VAL ILE GLN VAL SEQRES 5 A 588 TYR GLU GLU THR ALA GLY VAL ARG PRO GLY GLU PRO VAL SEQRES 6 A 588 VAL GLY THR GLY ALA SER LEU SER VAL GLU LEU GLY PRO SEQRES 7 A 588 ARG LEU LEU THR SER ILE TYR ASP GLY ILE GLN ARG PRO SEQRES 8 A 588 LEU GLU VAL ILE ARG GLU LYS THR GLY ASP PHE ILE ALA SEQRES 9 A 588 ARG GLY VAL THR ALA PRO ALA LEU PRO ARG ASP LYS LYS SEQRES 10 A 588 TRP HIS PHE ILE PRO LYS ALA LYS VAL GLY ASP LYS VAL SEQRES 11 A 588 VAL GLY GLY ASP ILE ILE GLY GLU VAL PRO GLU THR SER SEQRES 12 A 588 ILE ILE VAL HIS LYS ILE MET VAL PRO PRO GLY ILE GLU SEQRES 13 A 588 GLY GLU ILE VAL GLU ILE ALA GLU GLU GLY ASP TYR THR SEQRES 14 A 588 ILE GLU GLU VAL ILE ALA LYS VAL LYS THR PRO SER GLY SEQRES 15 A 588 GLU ILE LYS GLU LEU LYS MET TYR GLN ARG TRP PRO VAL SEQRES 16 A 588 ARG VAL LYS ARG PRO TYR LYS GLU LYS LEU PRO PRO GLU SEQRES 17 A 588 VAL PRO LEU ILE THR GLY GLN ARG VAL ILE ASP THR PHE SEQRES 18 A 588 PHE PRO GLN ALA LYS GLY GLY THR ALA ALA ILE PRO GLY SEQRES 19 A 588 PRO PHE GLY SER GLY LYS THR VAL THR GLN HIS GLN LEU SEQRES 20 A 588 ALA LYS TRP SER ASP ALA GLN VAL VAL ILE TYR ILE GLY SEQRES 21 A 588 CYS GLY GLU ARG GLY ASN GLU MET THR ASP VAL LEU GLU SEQRES 22 A 588 GLU PHE PRO LYS LEU LYS ASP PRO LYS THR GLY LYS PRO SEQRES 23 A 588 LEU MET GLU ARG THR VAL LEU ILE ALA ASN THR SER ASN SEQRES 24 A 588 MET PRO VAL ALA ALA ARG GLU ALA SER ILE TYR THR GLY SEQRES 25 A 588 ILE THR ILE ALA GLU TYR PHE ARG ASP MET GLY TYR ASP SEQRES 26 A 588 VAL ALA LEU MET ALA ASP SER THR SER ARG TRP ALA GLU SEQRES 27 A 588 ALA LEU ARG GLU ILE SER GLY ARG LEU GLU GLU MET PRO SEQRES 28 A 588 GLY GLU GLU GLY TYR PRO ALA TYR LEU ALA SER LYS LEU SEQRES 29 A 588 ALA GLU PHE TYR GLU ARG ALA GLY ARG VAL VAL THR LEU SEQRES 30 A 588 GLY SER ASP TYR ARG VAL GLY SER VAL SER VAL ILE GLY SEQRES 31 A 588 ALA VAL SER PRO PRO GLY GLY ASP PHE SER GLU PRO VAL SEQRES 32 A 588 VAL GLN ASN THR LEU ARG VAL VAL LYS VAL PHE TRP ALA SEQRES 33 A 588 LEU ASP ALA ASP LEU ALA ARG ARG ARG HIS PHE PRO ALA SEQRES 34 A 588 ILE ASN TRP LEU THR SER TYR SER LEU TYR VAL ASP ALA SEQRES 35 A 588 VAL LYS ASP TRP TRP HIS LYS ASN ILE ASP PRO GLU TRP SEQRES 36 A 588 LYS ALA MET ARG ASP LYS ALA MET ALA LEU LEU GLN LYS SEQRES 37 A 588 GLU SER GLU LEU GLN GLU ILE VAL ARG ILE VAL GLY PRO SEQRES 38 A 588 ASP ALA LEU PRO GLU ARG GLU ARG ALA ILE LEU LEU VAL SEQRES 39 A 588 ALA ARG MET LEU ARG GLU ASP TYR LEU GLN GLN ASP ALA SEQRES 40 A 588 PHE ASP GLU VAL ASP THR TYR CYS PRO PRO GLU LYS GLN SEQRES 41 A 588 VAL THR MET MET ARG VAL LEU LEU ASN PHE TYR ASP LYS SEQRES 42 A 588 THR MET GLU ALA ILE ASN ARG GLY VAL PRO LEU GLU GLU SEQRES 43 A 588 ILE ALA LYS LEU PRO VAL ARG GLU GLU ILE GLY ARG MET SEQRES 44 A 588 LYS PHE GLU ARG ASP VAL SER LYS ILE ARG SER LEU ILE SEQRES 45 A 588 ASP LYS THR ASN GLU GLN PHE GLU GLU LEU PHE LYS LYS SEQRES 46 A 588 TYR GLY ALA HET ADP A 589 27 HET MPD A 590 8 HET MPD A 591 8 HET MPD A 592 8 HET TRS A 593 8 HET ACY A 594 4 HETNAM ADP ADENOSINE-5'-DIPHOSPHATE HETNAM MPD (4S)-2-METHYL-2,4-PENTANEDIOL HETNAM TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL HETNAM ACY ACETIC ACID HETSYN TRS TRIS BUFFER FORMUL 2 ADP C10 H15 N5 O10 P2 FORMUL 3 MPD 3(C6 H14 O2) FORMUL 6 TRS C4 H12 N O3 1+ FORMUL 7 ACY C2 H4 O2 FORMUL 8 HOH *295(H2 O) HELIX 1 1 GLN A 215 PHE A 222 1 8 HELIX 2 2 VAL A 242 SER A 251 1 10 HELIX 3 3 ARG A 264 MET A 268 5 5 HELIX 4 4 PRO A 286 GLU A 289 5 4 HELIX 5 5 PRO A 301 MET A 322 1 22 HELIX 6 6 PRO A 357 GLU A 369 1 13 HELIX 7 7 PRO A 402 LEU A 408 1 7 HELIX 8 8 ASP A 418 ARG A 424 1 7 HELIX 9 9 TYR A 439 ILE A 451 1 13 HELIX 10 10 GLU A 454 GLY A 480 1 27 HELIX 11 11 PRO A 485 TYR A 502 1 18 HELIX 12 12 PRO A 516 ASN A 539 1 24 HELIX 13 13 PRO A 543 ALA A 548 1 6 HELIX 14 14 PRO A 551 MET A 559 1 9 HELIX 15 15 LYS A 560 GLU A 562 5 3 HELIX 16 16 ASP A 564 SER A 570 1 7 HELIX 17 17 SER A 570 GLY A 587 1 18 SHEET 1 A 2 SER A 73 LEU A 76 0 SHEET 2 A 2 GLN A 191 PRO A 194 -1 O GLN A 191 N LEU A 76 SHEET 1 B 7 ILE A 84 TYR A 85 0 SHEET 2 B 7 THR A 291 ILE A 294 1 O LEU A 293 N TYR A 85 SHEET 3 B 7 VAL A 255 ILE A 259 1 N TYR A 258 O ILE A 294 SHEET 4 B 7 ASP A 325 ALA A 330 1 O MET A 329 N ILE A 259 SHEET 5 B 7 VAL A 383 VAL A 392 1 O ALA A 391 N ALA A 330 SHEET 6 B 7 GLY A 372 VAL A 375 -1 N VAL A 374 O GLY A 384 SHEET 7 B 7 GLU A 203 LYS A 204 -1 N GLU A 203 O VAL A 375 SHEET 1 C 8 ILE A 84 TYR A 85 0 SHEET 2 C 8 THR A 291 ILE A 294 1 O LEU A 293 N TYR A 85 SHEET 3 C 8 VAL A 255 ILE A 259 1 N TYR A 258 O ILE A 294 SHEET 4 C 8 ASP A 325 ALA A 330 1 O MET A 329 N ILE A 259 SHEET 5 C 8 VAL A 383 VAL A 392 1 O ALA A 391 N ALA A 330 SHEET 6 C 8 THR A 229 PRO A 233 1 N ALA A 230 O GLY A 390 SHEET 7 C 8 VAL A 413 PHE A 414 1 O VAL A 413 N ALA A 231 SHEET 8 C 8 TYR A 436 SER A 437 -1 O TYR A 436 N PHE A 414 SHEET 1 D 4 VAL A 146 MET A 150 0 SHEET 2 D 4 ILE A 135 PRO A 140 -1 N VAL A 139 O HIS A 147 SHEET 3 D 4 TRP A 118 PRO A 122 -1 N ILE A 121 O GLU A 138 SHEET 4 D 4 GLY A 166 TYR A 168 -1 O GLY A 166 N PHE A 120 SHEET 1 E 4 LYS A 129 VAL A 130 0 SHEET 2 E 4 GLY A 157 ILE A 162 -1 O GLY A 157 N VAL A 130 SHEET 3 E 4 ALA A 175 LYS A 178 -1 O LYS A 178 N GLU A 158 SHEET 4 E 4 ILE A 184 LEU A 187 -1 O LYS A 185 N VAL A 177 SHEET 1 F 2 PRO A 210 LEU A 211 0 SHEET 2 F 2 GLN A 224 ALA A 225 -1 O GLN A 224 N LEU A 211 SITE 1 AC1 21 LYS A 240 THR A 241 VAL A 242 THR A 243 SITE 2 AC1 21 LEU A 417 ASP A 418 ALA A 419 ALA A 422 SITE 3 AC1 21 PHE A 427 PRO A 428 ALA A 429 ALA A 483 SITE 4 AC1 21 PRO A 485 GLN A 505 ASP A 506 ALA A 507 SITE 5 AC1 21 PHE A 508 HOH A 781 HOH A 845 HOH A 858 SITE 6 AC1 21 HOH A 859 SITE 1 AC2 4 GLN A 246 LYS A 249 ILE A 475 PHE A 508 SITE 1 AC3 6 ASP A 420 ASN A 431 TRP A 432 LEU A 433 SITE 2 AC3 6 HOH A 648 HOH A 650 SITE 1 AC4 5 MET A 458 LYS A 461 LEU A 528 ASP A 532 SITE 2 AC4 5 HOH A 771 SITE 1 AC5 4 GLU A 183 ILE A 184 PRO A 551 GLU A 581 SITE 1 AC6 3 PHE A 399 LEU A 417 HOH A 691 CRYST1 128.472 128.472 104.991 90.00 90.00 90.00 P 43 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 0.007784 0.000000 0.000000 0.00000 SCALE2 0.000000 0.007784 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009525 0.00000