HEADER ELECTRON TRANSPORT 12-MAY-99 1QHE TITLE ENERGETICS OF A HYDROGEN BOND (CHARGED AND NEUTRAL) AND OF A CATION-PI TITLE 2 INTERACTION IN APOFLAVODOXIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN (FLAVODOXIN); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: NOSTOC SP.; SOURCE 3 ORGANISM_TAXID: 1168; SOURCE 4 STRAIN: PCC 7119; SOURCE 5 CELL_LINE: E.COLI JM109; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: TG1; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PTRC99A KEYWDS FLAVODOXIN, ELECTRON TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR A.ROMERO,J.FERNANDEZ-RECIO,J.SANCHO REVDAT 6 16-AUG-23 1QHE 1 REMARK REVDAT 5 13-JUL-11 1QHE 1 VERSN REVDAT 4 24-FEB-09 1QHE 1 VERSN REVDAT 3 01-APR-03 1QHE 1 JRNL REVDAT 2 23-DEC-99 1QHE 1 JRNL HEADER REVDAT 1 20-MAY-99 1QHE 0 JRNL AUTH J.FERNANDEZ-RECIO,A.ROMERO,J.SANCHO JRNL TITL ENERGETICS OF A HYDROGEN BOND (CHARGED AND NEUTRAL) AND OF A JRNL TITL 2 CATION-PI INTERACTION IN APOFLAVODOXIN. JRNL REF J.MOL.BIOL. V. 290 319 1999 JRNL REFN ISSN 0022-2836 JRNL PMID 10388575 JRNL DOI 10.1006/JMBI.1999.2863 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH C.G.GENZOR,A.PERALES-ALCON,J.SANCHO,A.ROMERO REMARK 1 TITL STRUCTURE OF APOFLAVODOXIN: CLOSURE OF A TYROSINE/TRYPTOPHAN REMARK 1 TITL 2 AROMATIC GATE LEADS TO A COMPACT FOLD REMARK 1 REF NAT.STRUCT.BIOL. V. 3 329 1996 REMARK 1 REFN ISSN 1072-8368 REMARK 1 REFERENCE 2 REMARK 1 AUTH S.T.RAO,F.SHAFFIE,C.YU,K.A.SATYSHUR,B.J.STOCKMAN, REMARK 1 AUTH 2 J.L.MARKLEY,M.SUNDARLINGAM REMARK 1 TITL STRUCTURE OF THE OXIDIZED LONG-CHAIN FLAVODOXIN FROM REMARK 1 TITL 2 ANABAENA 7120 AT 2 A RESOLUTION REMARK 1 REF PROTEIN SCI. V. 1 1413 1992 REMARK 1 REFN ISSN 0961-8368 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.851 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 8.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 91.0 REMARK 3 NUMBER OF REFLECTIONS : 8242 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 SET) : 0.181 REMARK 3 FREE R VALUE : 0.257 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 499 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 8 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.09 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 65.00 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 496 REMARK 3 BIN R VALUE (WORKING SET) : 0.2430 REMARK 3 BIN FREE R VALUE : 0.3060 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : 45 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1326 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 5 REMARK 3 SOLVENT ATOMS : 90 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 14.52 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.009 REMARK 3 BOND ANGLES (DEGREES) : 1.517 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 25.79 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.343 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.500 ; 1.700 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.000 ; 2.300 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.000 ; 2.200 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 2.500 ; 2.800 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PARAMCSDX.PRO REMARK 3 PARAMETER FILE 2 : PARAM19.SOL REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : TOPHCSD.PRO REMARK 3 TOPOLOGY FILE 2 : AMTOPH19.SO REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1QHE COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 17-MAY-99. REMARK 100 THE DEPOSITION ID IS D_1000001053. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 293 REMARK 200 PH : 9.0 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 RU200 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : CCP4 (ROTAVATA) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 8777 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 91.8 REMARK 200 DATA REDUNDANCY : 4.600 REMARK 200 R MERGE (I) : 0.05100 REMARK 200 R SYM (I) : 0.09500 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 6.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.11 REMARK 200 COMPLETENESS FOR SHELL (%) : 63.2 REMARK 200 DATA REDUNDANCY IN SHELL : 4.20 REMARK 200 R MERGE FOR SHELL (I) : 0.05500 REMARK 200 R SYM FOR SHELL (I) : 0.19700 REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: PDB ENTRY 1FTG REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 30.70 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.80 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 3.2 M AMMONIUM SULPHATE, 0.1 M NA-K REMARK 280 PHOSPHATE PH = 9.0. CRYSTALS OF APOFLAVODOXIN APPEARED WITHIN 2 REMARK 280 MONTHS., PH 9.0 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 27.78000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 31.39500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 19.30000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 31.39500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 27.78000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 19.30000 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 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 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 LEU A 6 CA - CB - CG ANGL. DEV. = 14.0 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 ILE A 59 -5.78 -50.72 REMARK 500 ASN A 97 33.86 -140.26 REMARK 500 ASN A 128 -65.74 -99.51 REMARK 500 ASN A 135 -57.59 114.30 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 SO4 A 700 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1FTG RELATED DB: PDB REMARK 900 STRUCTURE OF APOFLAVODOXIN AT PH 6.0 DBREF 1QHE A 2 169 UNP P0A3E0 FLAV_ANASO 2 169 SEQRES 1 A 168 LYS LYS ILE GLY LEU PHE TYR GLY THR GLN THR GLY LYS SEQRES 2 A 168 THR GLU SER VAL ALA GLU ILE ILE ARG ASP GLU PHE GLY SEQRES 3 A 168 ASN ASP VAL VAL THR LEU HIS ASP VAL SER GLN ALA GLU SEQRES 4 A 168 VAL THR ASP LEU ASN ASP TYR GLN TYR LEU ILE ILE GLY SEQRES 5 A 168 CYS PRO THR TRP ASN ILE GLY GLU LEU GLN SER ASP TRP SEQRES 6 A 168 GLU GLY LEU TYR SER GLU LEU ASP ASP VAL ASP PHE ASN SEQRES 7 A 168 GLY LYS LEU VAL ALA TYR PHE GLY THR GLY ASP GLN ILE SEQRES 8 A 168 GLY TYR ALA ASP ASN PHE GLN ASP ALA ILE GLY ILE LEU SEQRES 9 A 168 GLU GLU LYS ILE SER GLN ARG GLY GLY LYS THR VAL GLY SEQRES 10 A 168 TYR TRP SER THR ASP GLY TYR ASP PHE ASN ASP SER LYS SEQRES 11 A 168 ALA LEU ARG ASN GLY LYS PHE VAL GLY LEU ALA LEU ASP SEQRES 12 A 168 GLU ASP ASN GLN SER ASP LEU THR ASP ASP ARG ILE LYS SEQRES 13 A 168 SER TRP VAL ALA GLN LEU LYS SER GLU PHE GLY LEU HET SO4 A 700 5 HETNAM SO4 SULFATE ION FORMUL 2 SO4 O4 S 2- FORMUL 3 HOH *90(H2 O) HELIX 1 1 LYS A 14 PHE A 26 1 13 HELIX 2 2 VAL A 36 GLN A 38 5 3 HELIX 3 3 VAL A 41 ASP A 46 5 6 HELIX 4 4 SER A 64 ASP A 75 1 12 HELIX 5 5 ASP A 100 GLN A 111 1 12 HELIX 6 6 THR A 152 PHE A 167 1 16 SHEET 1 A 5 VAL A 31 ASP A 35 0 SHEET 2 A 5 ILE A 4 TYR A 8 1 N ILE A 4 O THR A 32 SHEET 3 A 5 TYR A 49 GLY A 53 1 N TYR A 49 O GLY A 5 SHEET 4 A 5 LEU A 82 THR A 88 1 N LEU A 82 O LEU A 50 SHEET 5 A 5 LEU A 141 LEU A 143 1 N LEU A 141 O GLY A 87 SITE 1 AC1 10 THR A 10 GLN A 11 THR A 12 GLY A 13 SITE 2 AC1 10 LYS A 14 THR A 15 PRO A 55 TRP A 57 SITE 3 AC1 10 THR A 88 HOH A 556 CRYST1 55.560 38.600 62.790 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 0.017998 0.000000 0.000000 0.00000 SCALE2 0.000000 0.025907 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015926 0.00000