PDB Short entry for 2PTF HEADER STRUCTURAL GENOMICS, UNKNOWN FUNCTION 08-MAY-07 2PTF TITLE CRYSTAL STRUCTURE OF PROTEIN MTH_863 FROM METHANOBACTERIUM TITLE 2 THERMOAUTOTROPHICUM BOUND TO FMN COMPND MOL_ID: 1; COMPND 2 MOLECULE: UNCHARACTERIZED PROTEIN MTH_863; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: METHANOTHERMOBACTER THERMAUTOTROPHICUS; SOURCE 3 ORGANISM_TAXID: 187420; SOURCE 4 STRAIN: DELTA H; SOURCE 5 GENE: MTH_863; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_VECTOR: PET; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: MODIFIED PET26 KEYWDS STRUCTURAL GENOMICS, UNKNOWN FUNCTION, PSI-2, PROTEIN STRUCTURE KEYWDS 2 INITIATIVE, NEW YORK SGX RESEARCH CENTER FOR STRUCTURAL GENOMICS, KEYWDS 3 NYSGXRC EXPDTA X-RAY DIFFRACTION AUTHOR J.B.BONANNO,M.RUTTER,K.T.BAIN,M.IIZUKA,S.OZYURT,D.SMITH,S.WASSERMAN, AUTHOR 2 J.M.SAUDER,S.K.BURLEY,S.C.ALMO,NEW YORK SGX RESEARCH CENTER FOR AUTHOR 3 STRUCTURAL GENOMICS (NYSGXRC) REVDAT 8 21-FEB-24 2PTF 1 REMARK REVDAT 7 03-FEB-21 2PTF 1 AUTHOR JRNL REMARK SEQADV REVDAT 6 14-NOV-18 2PTF 1 AUTHOR REVDAT 5 18-OCT-17 2PTF 1 REMARK REVDAT 4 24-OCT-12 2PTF 1 AUTHOR REVDAT 3 13-JUL-11 2PTF 1 VERSN REVDAT 2 24-FEB-09 2PTF 1 VERSN REVDAT 1 15-MAY-07 2PTF 0 JRNL AUTH J.B.BONANNO,M.RUTTER,K.T.BAIN,M.IIZUKA,S.OZYURT,D.SMITH, JRNL AUTH 2 S.WASSERMAN,J.M.SAUDER,S.K.BURLEY,S.C.ALMO JRNL TITL CRYSTAL STRUCTURE OF PROTEIN MTH_863 FROM METHANOBACTERIUM JRNL TITL 2 THERMOAUTOTROPHICUM BOUND TO FMN. JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.35 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) : 2.35 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 21546 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) : 0.201 REMARK 3 R VALUE (WORKING SET) : 0.199 REMARK 3 FREE R VALUE : 0.253 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1092 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) : 2.35 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.41 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1469 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.1950 REMARK 3 BIN FREE R VALUE SET COUNT : 84 REMARK 3 BIN FREE R VALUE : 0.2640 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3189 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 62 REMARK 3 SOLVENT ATOMS : 118 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 38.60 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 41.36 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.10000 REMARK 3 B22 (A**2) : -1.10000 REMARK 3 B33 (A**2) : 2.20000 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): 0.332 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.246 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.160 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 6.397 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.940 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.898 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3316 ; 0.018 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4488 ; 1.568 ; 1.983 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 399 ; 6.593 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 162 ;32.876 ;22.654 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 580 ;16.565 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 39 ;18.933 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 512 ; 0.103 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2468 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1367 ; 0.206 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2284 ; 0.303 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 178 ; 0.175 ; 0.200 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): 17 ; 0.200 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 2 ; 0.138 ; 0.200 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): 2046 ; 1.175 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3202 ; 1.944 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1500 ; 3.182 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1284 ; 5.105 ; 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 : BABINET MODEL WITH 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 REMARK 4 REMARK 4 2PTF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-MAY-07. REMARK 100 THE DEPOSITION ID IS D_1000042758. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-MAY-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 : NSLS REMARK 200 BEAMLINE : X29A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9791 REMARK 200 MONOCHROMATOR : SI REMARK 200 OPTICS : NULL 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 : SCALA, CCP4 (SCALA) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 21594 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.350 REMARK 200 RESOLUTION RANGE LOW (A) : 45.883 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 12.50 REMARK 200 R MERGE (I) : 0.08700 REMARK 200 R SYM (I) : 0.08700 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 26.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.35 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.48 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 12.80 REMARK 200 R MERGE FOR SHELL (I) : 0.41300 REMARK 200 R SYM FOR SHELL (I) : 0.41300 REMARK 200 <I/SIGMA(I)> FOR SHELL : 5.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SHELXCD, SHELXD REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.56 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.35 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM TRIS-HCL, 50% MPD, 100 MM REMARK 280 AMMONIUM PHOSPHATE, PH 8.5, VAPOR DIFFUSION, TEMPERATURE 294K 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 58.93400 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 45.86350 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 45.86350 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 29.46700 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 45.86350 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 45.86350 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 88.40100 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 45.86350 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 45.86350 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 29.46700 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 45.86350 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 45.86350 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 88.40100 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 58.93400 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: 5230 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19500 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -40.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 SER A 0 REMARK 465 LEU A 1 REMARK 465 SER A 2 REMARK 465 GLY A 3 REMARK 465 ALA A 4 REMARK 465 LEU A 5 REMARK 465 LYS A 6 REMARK 465 GLU A 7 REMARK 465 ASN A 8 REMARK 465 SER A 9 REMARK 465 GLY A 10 REMARK 465 LYS A 11 REMARK 465 PRO A 12 REMARK 465 SER A 13 REMARK 465 GLU A 14 REMARK 465 PHE A 138 REMARK 465 GLY A 139 REMARK 465 GLU A 181 REMARK 465 PHE A 182 REMARK 465 SER A 183 REMARK 465 ASP A 184 REMARK 465 LYS A 221 REMARK 465 ILE A 222 REMARK 465 SER A 223 REMARK 465 GLU A 224 REMARK 465 GLY A 225 REMARK 465 HIS A 226 REMARK 465 HIS A 227 REMARK 465 HIS A 228 REMARK 465 HIS A 229 REMARK 465 HIS A 230 REMARK 465 HIS A 231 REMARK 465 MET B -1 REMARK 465 SER B 0 REMARK 465 LEU B 1 REMARK 465 SER B 2 REMARK 465 GLY B 3 REMARK 465 ALA B 4 REMARK 465 LEU B 5 REMARK 465 LYS B 6 REMARK 465 GLU B 7 REMARK 465 ASN B 8 REMARK 465 SER B 9 REMARK 465 GLY B 10 REMARK 465 LYS B 11 REMARK 465 PRO B 12 REMARK 465 SER B 13 REMARK 465 GLU B 14 REMARK 465 LYS B 134 REMARK 465 ARG B 135 REMARK 465 ASP B 136 REMARK 465 ARG B 137 REMARK 465 PHE B 138 REMARK 465 GLY B 139 REMARK 465 LYS B 221 REMARK 465 ILE B 222 REMARK 465 SER B 223 REMARK 465 GLU B 224 REMARK 465 GLY B 225 REMARK 465 HIS B 226 REMARK 465 HIS B 227 REMARK 465 HIS B 228 REMARK 465 HIS B 229 REMARK 465 HIS B 230 REMARK 465 HIS B 231 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 OH TYR B 168 OE1 GLU B 172 2.04 REMARK 500 OE2 GLU B 172 O HOH B 355 2.05 REMARK 500 O HOH A 349 O HOH B 360 2.14 REMARK 500 REMARK 500 REMARK: NULL 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 GLU B 172 CB GLU B 172 CG -0.117 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 ARG A 110 -120.25 44.68 REMARK 500 ASP A 136 -166.48 -161.41 REMARK 500 ARG B 110 -125.91 37.59 REMARK 500 ARG B 160 -59.92 -128.16 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 FMN A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FMN B 301 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: NYSGXRC-10069I RELATED DB: TARGETDB DBREF 2PTF A 2 223 UNP O26951 Y863_METTH 2 223 DBREF 2PTF B 2 223 UNP O26951 Y863_METTH 2 223 SEQADV 2PTF MET A -1 UNP O26951 CLONING ARTIFACT SEQADV 2PTF SER A 0 UNP O26951 CLONING ARTIFACT SEQADV 2PTF LEU A 1 UNP O26951 CLONING ARTIFACT SEQADV 2PTF GLU A 224 UNP O26951 CLONING ARTIFACT SEQADV 2PTF GLY A 225 UNP O26951 CLONING ARTIFACT SEQADV 2PTF HIS A 226 UNP O26951 CLONING ARTIFACT SEQADV 2PTF HIS A 227 UNP O26951 CLONING ARTIFACT SEQADV 2PTF HIS A 228 UNP O26951 CLONING ARTIFACT SEQADV 2PTF HIS A 229 UNP O26951 CLONING ARTIFACT SEQADV 2PTF HIS A 230 UNP O26951 CLONING ARTIFACT SEQADV 2PTF HIS A 231 UNP O26951 CLONING ARTIFACT SEQADV 2PTF MET B -1 UNP O26951 CLONING ARTIFACT SEQADV 2PTF SER B 0 UNP O26951 CLONING ARTIFACT SEQADV 2PTF LEU B 1 UNP O26951 CLONING ARTIFACT SEQADV 2PTF GLU B 224 UNP O26951 CLONING ARTIFACT SEQADV 2PTF GLY B 225 UNP O26951 CLONING ARTIFACT SEQADV 2PTF HIS B 226 UNP O26951 CLONING ARTIFACT SEQADV 2PTF HIS B 227 UNP O26951 CLONING ARTIFACT SEQADV 2PTF HIS B 228 UNP O26951 CLONING ARTIFACT SEQADV 2PTF HIS B 229 UNP O26951 CLONING ARTIFACT SEQADV 2PTF HIS B 230 UNP O26951 CLONING ARTIFACT SEQADV 2PTF HIS B 231 UNP O26951 CLONING ARTIFACT SEQRES 1 A 233 MET SER LEU SER GLY ALA LEU LYS GLU ASN SER GLY LYS SEQRES 2 A 233 PRO SER GLU VAL GLU TYR THR HIS PHE LYS ASP LEU GLN SEQRES 3 A 233 ALA LEU GLU MET GLU ARG GLY ARG LEU TYR GLU THR ILE SEQRES 4 A 233 VAL VAL THR TRP ASP ASP SER MET VAL GLY ASN ALA ALA SEQRES 5 A 233 PRO ILE GLY VAL LEU CYS THR GLY ASP ASP THR VAL THR SEQRES 6 A 233 LEU TYR LEU TYR GLN GLY THR ARG THR VAL GLU ASN VAL SEQRES 7 A 233 LEU ASN ASN GLY ARG PHE THR VAL ASN VAL THR LEU ASP SEQRES 8 A 233 PRO LEU ILE PHE THR ASP SER THR LEU GLY ASP LEU GLU SEQRES 9 A 233 GLU ASP MET PHE SER HIS TYR ARG ASP PHE LEU HIS LEU SEQRES 10 A 233 ARG GLY ALA ASP ALA PHE PHE THR ALA GLU VAL VAL SER SEQRES 11 A 233 VAL LYS LYS LEU VAL LYS ARG ASP ARG PHE GLY GLU SER SEQRES 12 A 233 GLU LEU HIS VAL VAL LYS ALA ARG ALA GLY ASP VAL MET SEQRES 13 A 233 ARG ALA GLU SER PHE ARG MET ALA LEU ASN ARG GLY ILE SEQRES 14 A 233 TYR ALA VAL ILE GLU SER LEU ILE ALA TYR THR ARG ALA SEQRES 15 A 233 GLU PHE SER ASP PRO LEU VAL LEU ARG GLU ARG ILE ALA SEQRES 16 A 233 GLU MET ASN ARG VAL ALA ARG LYS VAL GLY GLY PRO ARG SEQRES 17 A 233 GLU LYS GLU ALA MET ARG ARG ILE ILE GLN ALA LEU GLU SEQRES 18 A 233 SER LYS ILE SER GLU GLY HIS HIS HIS HIS HIS HIS SEQRES 1 B 233 MET SER LEU SER GLY ALA LEU LYS GLU ASN SER GLY LYS SEQRES 2 B 233 PRO SER GLU VAL GLU TYR THR HIS PHE LYS ASP LEU GLN SEQRES 3 B 233 ALA LEU GLU MET GLU ARG GLY ARG LEU TYR GLU THR ILE SEQRES 4 B 233 VAL VAL THR TRP ASP ASP SER MET VAL GLY ASN ALA ALA SEQRES 5 B 233 PRO ILE GLY VAL LEU CYS THR GLY ASP ASP THR VAL THR SEQRES 6 B 233 LEU TYR LEU TYR GLN GLY THR ARG THR VAL GLU ASN VAL SEQRES 7 B 233 LEU ASN ASN GLY ARG PHE THR VAL ASN VAL THR LEU ASP SEQRES 8 B 233 PRO LEU ILE PHE THR ASP SER THR LEU GLY ASP LEU GLU SEQRES 9 B 233 GLU ASP MET PHE SER HIS TYR ARG ASP PHE LEU HIS LEU SEQRES 10 B 233 ARG GLY ALA ASP ALA PHE PHE THR ALA GLU VAL VAL SER SEQRES 11 B 233 VAL LYS LYS LEU VAL LYS ARG ASP ARG PHE GLY GLU SER SEQRES 12 B 233 GLU LEU HIS VAL VAL LYS ALA ARG ALA GLY ASP VAL MET SEQRES 13 B 233 ARG ALA GLU SER PHE ARG MET ALA LEU ASN ARG GLY ILE SEQRES 14 B 233 TYR ALA VAL ILE GLU SER LEU ILE ALA TYR THR ARG ALA SEQRES 15 B 233 GLU PHE SER ASP PRO LEU VAL LEU ARG GLU ARG ILE ALA SEQRES 16 B 233 GLU MET ASN ARG VAL ALA ARG LYS VAL GLY GLY PRO ARG SEQRES 17 B 233 GLU LYS GLU ALA MET ARG ARG ILE ILE GLN ALA LEU GLU SEQRES 18 B 233 SER LYS ILE SER GLU GLY HIS HIS HIS HIS HIS HIS HET FMN A 301 31 HET FMN B 301 31 HETNAM FMN FLAVIN MONONUCLEOTIDE HETSYN FMN RIBOFLAVIN MONOPHOSPHATE FORMUL 3 FMN 2(C17 H21 N4 O9 P) FORMUL 5 HOH *118(H2 O) HELIX 1 1 ASP A 22 LEU A 26 5 5 HELIX 2 2 THR A 70 GLY A 80 1 11 HELIX 3 3 ASP A 89 GLY A 99 1 11 HELIX 4 4 GLU A 102 ASP A 104 5 3 HELIX 5 5 ARG A 165 ARG A 179 1 15 HELIX 6 6 PRO A 185 GLY A 203 1 19 HELIX 7 7 GLY A 204 SER A 220 1 17 HELIX 8 8 ASP B 22 GLU B 27 5 6 HELIX 9 9 THR B 70 GLY B 80 1 11 HELIX 10 10 ASP B 89 GLY B 99 1 11 HELIX 11 11 GLU B 102 ASP B 104 5 3 HELIX 12 12 ARG B 165 ARG B 179 1 15 HELIX 13 13 ALA B 180 SER B 183 5 4 HELIX 14 14 ASP B 184 GLY B 203 1 20 HELIX 15 15 GLY B 204 SER B 220 1 17 SHEET 1 A 8 THR A 18 PHE A 20 0 SHEET 2 A 8 SER A 141 ARG A 155 -1 O VAL A 153 N PHE A 20 SHEET 3 A 8 ALA A 120 LYS A 134 -1 N LYS A 134 O SER A 141 SHEET 4 A 8 ARG A 81 VAL A 86 -1 N VAL A 86 O ALA A 120 SHEET 5 A 8 LEU A 33 TRP A 41 -1 N ILE A 37 O ASN A 85 SHEET 6 A 8 GLY A 47 CYS A 56 -1 O ALA A 50 N VAL A 38 SHEET 7 A 8 THR A 61 TYR A 67 -1 O THR A 63 N LEU A 55 SHEET 8 A 8 SER A 141 ARG A 155 -1 O ALA A 148 N VAL A 62 SHEET 1 B 2 PHE A 106 TYR A 109 0 SHEET 2 B 2 PHE A 112 LEU A 115 -1 O HIS A 114 N SER A 107 SHEET 1 C 8 TYR B 17 PHE B 20 0 SHEET 2 C 8 LEU B 143 ALA B 156 -1 O ARG B 155 N THR B 18 SHEET 3 C 8 ALA B 120 LEU B 132 -1 N LEU B 132 O LEU B 143 SHEET 4 C 8 ARG B 81 VAL B 86 -1 N VAL B 86 O ALA B 120 SHEET 5 C 8 LEU B 33 TRP B 41 -1 N ILE B 37 O ASN B 85 SHEET 6 C 8 GLY B 47 CYS B 56 -1 O ALA B 50 N VAL B 38 SHEET 7 C 8 THR B 61 TYR B 67 -1 O THR B 63 N LEU B 55 SHEET 8 C 8 LEU B 143 ALA B 156 -1 O HIS B 144 N LEU B 66 SHEET 1 D 2 PHE B 106 TYR B 109 0 SHEET 2 D 2 PHE B 112 LEU B 115 -1 O PHE B 112 N TYR B 109 SITE 1 AC1 13 ASN A 48 PRO A 51 ILE A 52 GLY A 53 SITE 2 AC1 13 TYR A 65 LEU A 66 TYR A 67 THR A 70 SITE 3 AC1 13 ARG A 71 THR A 72 HOH A 302 HOH A 330 SITE 4 AC1 13 LEU B 174 SITE 1 AC2 18 LEU A 174 GLU B 35 ASN B 48 ALA B 50 SITE 2 AC2 18 PRO B 51 ILE B 52 GLY B 53 TYR B 65 SITE 3 AC2 18 LEU B 66 TYR B 67 THR B 70 ARG B 71 SITE 4 AC2 18 THR B 72 HOH B 309 HOH B 326 HOH B 337 SITE 5 AC2 18 HOH B 343 HOH B 351 CRYST1 91.727 91.727 117.868 90.00 90.00 90.00 P 41 21 2 16 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 0.010902 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010902 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008484 0.00000