HEADER FLAVOENZYME 20-NOV-96 1NOX TITLE NADH OXIDASE FROM THERMUS THERMOPHILUS COMPND MOL_ID: 1; COMPND 2 MOLECULE: NADH OXIDASE; COMPND 3 CHAIN: A; COMPND 4 EC: 1.6.99.3; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMUS THERMOPHILUS; SOURCE 3 ORGANISM_TAXID: 300852; SOURCE 4 STRAIN: HB8; SOURCE 5 ATCC: 27634; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: JM109; SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PKK223-3; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PTNADOX KEYWDS FLAVOENZYME, FLAVOPROTEIN FMN, OXIDOREDUCTASE, THERMOPHILE EXPDTA X-RAY DIFFRACTION AUTHOR H.J.HECHT,H.ERDMANN,H.J.PARK,M.SPRINZL,R.D.SCHMID REVDAT 5 03-APR-24 1NOX 1 REMARK REVDAT 4 14-FEB-24 1NOX 1 REMARK REVDAT 3 13-JUL-11 1NOX 1 VERSN REVDAT 2 24-FEB-09 1NOX 1 VERSN REVDAT 1 12-MAR-97 1NOX 0 JRNL AUTH H.J.HECHT,H.ERDMANN,H.J.PARK,M.SPRINZL,R.D.SCHMID JRNL TITL CRYSTAL STRUCTURE OF NADH OXIDASE FROM THERMUS THERMOPHILUS. JRNL REF NAT.STRUCT.BIOL. V. 2 1109 1995 JRNL REFN ISSN 1072-8368 JRNL PMID 8846223 JRNL DOI 10.1038/NSB1295-1109 REMARK 2 REMARK 2 RESOLUTION. 1.59 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 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.59 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 21.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.2 REMARK 3 NUMBER OF REFLECTIONS : 28064 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING + TEST SET) : 0.190 REMARK 3 R VALUE (WORKING SET) : 0.182 REMARK 3 FREE R VALUE : 0.204 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 28064 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1571 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 31 REMARK 3 SOLVENT ATOMS : 93 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 18.20 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 23.30 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 OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): NULL REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): NULL REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA REMARK 3 BOND LENGTH (A) : 0.016 ; 0.020 REMARK 3 ANGLE DISTANCE (A) : 0.031 ; 0.040 REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : 0.033 ; 0.050 REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL REMARK 3 REMARK 3 PLANE RESTRAINT (A) : 0.025 ; 0.030 REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : 0.134 ; 0.150 REMARK 3 REMARK 3 NON-BONDED CONTACT RESTRAINTS. REMARK 3 SINGLE TORSION (A) : 0.173 ; 0.300 REMARK 3 MULTIPLE TORSION (A) : 0.274 ; 0.300 REMARK 3 H-BOND (X...Y) (A) : NULL ; NULL REMARK 3 H-BOND (X-H...Y) (A) : NULL ; NULL REMARK 3 REMARK 3 CONFORMATIONAL TORSION ANGLE RESTRAINTS. REMARK 3 SPECIFIED (DEGREES) : NULL ; NULL REMARK 3 PLANAR (DEGREES) : 4.100 ; 7.000 REMARK 3 STAGGERED (DEGREES) : 16.000; 15.000 REMARK 3 TRANSVERSE (DEGREES) : 29.700; 20.000 REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.651 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.423 ; 3.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.503 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 4.017 ; 3.000 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: FREE-R-VALUE INTRODUCED LATE IN REMARK 3 REFINEMENT. REMARK 4 REMARK 4 1NOX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000175357. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NOV-93 REMARK 200 TEMPERATURE (KELVIN) : 283 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : MPG/DESY, HAMBURG REMARK 200 BEAMLINE : BW6 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : MIRRORS 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 (AGROVATA, SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 28064 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.590 REMARK 200 RESOLUTION RANGE LOW (A) : NULL REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.2 REMARK 200 DATA REDUNDANCY : 3.900 REMARK 200 R MERGE (I) : 0.07100 REMARK 200 R SYM (I) : 0.06900 REMARK 200 FOR THE DATA SET : 6.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.59 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.68 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.3 REMARK 200 DATA REDUNDANCY IN SHELL : 3.80 REMARK 200 R MERGE FOR SHELL (I) : 0.07100 REMARK 200 R SYM FOR SHELL (I) : 0.07100 REMARK 200 FOR SHELL : 3.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: ISOMORPHOUS AND MOLECULAR REMARK 200 REPLACEMENT REMARK 200 SOFTWARE USED: X-PLOR REMARK 200 STARTING MODEL: MODEL FROM ISOMORPHOUS REPLACEMENT REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.40 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.05 M MES-TRIS BUFFER PH 6.0, 26 % REMARK 280 PEG 4000, 0.3 M NACL, 50 MM FMN REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X+1/2,Y+1/2,-Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 31.26500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 30.30000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 31.26500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 30.30000 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA,PQS REMARK 350 TOTAL BURIED SURFACE AREA: 8030 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 17180 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -39.0 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 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 60.60000 REMARK 350 BIOMT3 2 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 GLU A 2 REMARK 465 ALA A 3 REMARK 465 THR A 4 REMARK 465 LEU A 5 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 17 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 ARG A 18 NE - CZ - NH2 ANGL. DEV. = -3.6 DEGREES REMARK 500 ARG A 21 NE - CZ - NH1 ANGL. DEV. = 4.2 DEGREES REMARK 500 ARG A 22 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 TYR A 23 CB - CG - CD2 ANGL. DEV. = -7.7 DEGREES REMARK 500 ARG A 67 NE - CZ - NH2 ANGL. DEV. = -4.2 DEGREES REMARK 500 TYR A 150 CB - CG - CD1 ANGL. DEV. = 4.3 DEGREES REMARK 500 ARG A 166 CD - NE - CZ ANGL. DEV. = 8.6 DEGREES REMARK 500 ARG A 195 NE - CZ - NH1 ANGL. DEV. = 7.7 DEGREES REMARK 500 ARG A 195 NE - CZ - NH2 ANGL. DEV. = -5.3 DEGREES REMARK 500 LEU A 203 CA - CB - CG ANGL. DEV. = 20.8 DEGREES REMARK 500 ARG A 205 NE - CZ - NH1 ANGL. DEV. = 3.3 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 TRP A 47 18.83 59.58 REMARK 500 ALA A 70 34.11 -98.89 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: COF REMARK 800 EVIDENCE_CODE: UNKNOWN REMARK 800 SITE_DESCRIPTION: COFACTOR REMARK 800 REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FMN A 300 DBREF 1NOX A 1 205 UNP Q60049 NOX_THET8 1 205 SEQRES 1 A 205 MET GLU ALA THR LEU PRO VAL LEU ASP ALA LYS THR ALA SEQRES 2 A 205 ALA LEU LYS ARG ARG SER ILE ARG ARG TYR ARG LYS ASP SEQRES 3 A 205 PRO VAL PRO GLU GLY LEU LEU ARG GLU ILE LEU GLU ALA SEQRES 4 A 205 ALA LEU ARG ALA PRO SER ALA TRP ASN LEU GLN PRO TRP SEQRES 5 A 205 ARG ILE VAL VAL VAL ARG ASP PRO ALA THR LYS ARG ALA SEQRES 6 A 205 LEU ARG GLU ALA ALA PHE GLY GLN ALA HIS VAL GLU GLU SEQRES 7 A 205 ALA PRO VAL VAL LEU VAL LEU TYR ALA ASP LEU GLU ASP SEQRES 8 A 205 ALA LEU ALA HIS LEU ASP GLU VAL ILE HIS PRO GLY VAL SEQRES 9 A 205 GLN GLY GLU ARG ARG GLU ALA GLN LYS GLN ALA ILE GLN SEQRES 10 A 205 ARG ALA PHE ALA ALA MET GLY GLN GLU ALA ARG LYS ALA SEQRES 11 A 205 TRP ALA SER GLY GLN SER TYR ILE LEU LEU GLY TYR LEU SEQRES 12 A 205 LEU LEU LEU LEU GLU ALA TYR GLY LEU GLY SER VAL PRO SEQRES 13 A 205 MET LEU GLY PHE ASP PRO GLU ARG VAL ARG ALA ILE LEU SEQRES 14 A 205 GLY LEU PRO SER ARG ALA ALA ILE PRO ALA LEU VAL ALA SEQRES 15 A 205 LEU GLY TYR PRO ALA GLU GLU GLY TYR PRO SER HIS ARG SEQRES 16 A 205 LEU PRO LEU GLU ARG VAL VAL LEU TRP ARG HET FMN A 300 31 HETNAM FMN FLAVIN MONONUCLEOTIDE HETSYN FMN RIBOFLAVIN MONOPHOSPHATE FORMUL 2 FMN C17 H21 N4 O9 P FORMUL 3 HOH *93(H2 O) HELIX 1 1 ALA A 10 LYS A 16 1 7 HELIX 2 2 GLU A 30 ARG A 42 1 13 HELIX 3 3 ALA A 46 ASN A 48 5 3 HELIX 4 4 PRO A 60 ALA A 69 1 10 HELIX 5 5 ALA A 74 GLU A 78 1 5 HELIX 6 6 LEU A 89 GLU A 98 1 10 HELIX 7 7 GLU A 107 ALA A 121 1 15 HELIX 8 8 GLN A 125 ALA A 149 1 25 HELIX 9 9 PRO A 162 LEU A 169 1 8 HELIX 10 10 LEU A 198 VAL A 201 1 4 SHEET 1 A 4 TRP A 52 VAL A 57 0 SHEET 2 A 4 VAL A 81 ALA A 87 -1 N TYR A 86 O ARG A 53 SHEET 3 A 4 ALA A 179 GLY A 184 -1 N LEU A 183 O VAL A 81 SHEET 4 A 4 GLY A 153 MET A 157 -1 N MET A 157 O LEU A 180 SITE 1 COF 1 FMN A 300 SITE 1 AC1 21 ARG A 17 ARG A 18 SER A 19 ARG A 21 SITE 2 AC1 21 PRO A 44 SER A 45 ALA A 46 ASN A 48 SITE 3 AC1 21 GLN A 73 GLN A 135 PRO A 156 MET A 157 SITE 4 AC1 21 LEU A 158 GLY A 159 SER A 193 ARG A 195 SITE 5 AC1 21 HOH A 302 HOH A 303 HOH A 311 HOH A 353 SITE 6 AC1 21 HOH A 373 CRYST1 62.530 60.600 56.660 90.00 90.00 90.00 P 21 21 2 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 0.015992 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016502 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017649 0.00000