HEADER OXIDOREDUCTASE 01-JUN-03 1PJ6 TITLE CRYSTAL STRUCTURE OF DIMETHYLGLYCINE OXIDASE OF ARTHROBACTER TITLE 2 GLOBIFORMIS IN COMPLEX WITH FOLIC ACID COMPND MOL_ID: 1; COMPND 2 MOLECULE: N,N-DIMETHYLGLYCINE OXIDASE; COMPND 3 CHAIN: A; COMPND 4 EC: 1.5.3.10; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ARTHROBACTER GLOBIFORMIS; SOURCE 3 ORGANISM_TAXID: 1665; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PUC19 KEYWDS CHANNELLING, FOLATE BINDING, FAD BINDING, AMINE OXIDATION, KEYWDS 2 OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR D.LEYS,J.BASRAN,N.S.SCRUTTON REVDAT 4 16-AUG-23 1PJ6 1 REMARK LINK REVDAT 3 13-JUL-11 1PJ6 1 VERSN REVDAT 2 24-FEB-09 1PJ6 1 VERSN REVDAT 1 07-OCT-03 1PJ6 0 JRNL AUTH D.LEYS,J.BASRAN,N.S.SCRUTTON JRNL TITL CHANNELLING AND FORMATION OF 'ACTIVE' FORMALDEHYDE IN JRNL TITL 2 DIMETHYLGLYCINE OXIDASE. JRNL REF EMBO J. V. 22 4038 2003 JRNL REFN ISSN 0261-4189 JRNL PMID 12912903 JRNL DOI 10.1093/EMBOJ/CDG395 REMARK 2 REMARK 2 RESOLUTION. 1.65 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.1.08 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) : 1.65 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 14.84 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 106504 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) : 0.158 REMARK 3 R VALUE (WORKING SET) : 0.156 REMARK 3 FREE R VALUE : 0.193 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 5618 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) : 1.65 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.69 REMARK 3 REFLECTION IN BIN (WORKING SET) : 7704 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2120 REMARK 3 BIN FREE R VALUE SET COUNT : 426 REMARK 3 BIN FREE R VALUE : 0.2420 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6285 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 86 REMARK 3 SOLVENT ATOMS : 1612 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.25 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.02000 REMARK 3 B22 (A**2) : -0.02000 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): 0.086 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.089 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.054 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.568 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.974 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.960 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6524 ; 0.016 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 8896 ; 1.634 ; 1.969 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 827 ; 5.951 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 990 ;12.159 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 986 ; 0.117 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5006 ; 0.009 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 3179 ; 0.220 ; 0.200 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): 1165 ; 0.166 ; 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): 45 ; 0.294 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 84 ; 0.203 ; 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): 4107 ; 0.923 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 6572 ; 1.582 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2417 ; 2.530 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2324 ; 4.049 ; 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: NULL REMARK 4 REMARK 4 1PJ6 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-JUN-03. REMARK 100 THE DEPOSITION ID IS D_1000019353. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-MAY-02 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : EMBL/DESY, HAMBURG REMARK 200 BEAMLINE : X11 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9 REMARK 200 MONOCHROMATOR : SYCHROTRON REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 106504 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.650 REMARK 200 RESOLUTION RANGE LOW (A) : 15.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 200 DATA REDUNDANCY : 5.400 REMARK 200 R MERGE (I) : 0.06700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.65 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.70 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL 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: 1PJ5 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.87 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.61 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 15% PEG 2000MME, 0.2 MGCL2, PH 7.5, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 294K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 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,Y,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z REMARK 290 7555 -X+1/2,Y+1/2,-Z REMARK 290 8555 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 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 35.43850 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 111.25300 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 35.43850 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 111.25300 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 35.43850 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 111.25300 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 35.43850 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 111.25300 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 300 REMARK: DMGO IS A TETRAMER (DIMER OF DIMERS) FORMED BY APPLYING THE REMARK 300 222 POINT SYMMETRY OF THE C222 SPACEGROUP 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 18440 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 112050 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -130.0 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 70.87700 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 222.50600 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -1.000000 0.000000 0.000000 70.87700 REMARK 350 BIOMT2 3 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 -1.000000 119.30400 REMARK 350 BIOMT1 4 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 4 0.000000 -1.000000 0.000000 222.50600 REMARK 350 BIOMT3 4 0.000000 0.000000 -1.000000 119.30400 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PQS 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 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 A3535 LIES ON A SPECIAL POSITION. REMARK 375 HOH A3664 LIES ON A SPECIAL POSITION. REMARK 375 HOH A3665 LIES ON A SPECIAL POSITION. REMARK 375 HOH A3671 LIES ON A SPECIAL POSITION. REMARK 375 HOH A3746 LIES ON A SPECIAL POSITION. REMARK 375 HOH A3865 LIES ON A SPECIAL POSITION. REMARK 375 HOH A4018 LIES ON A SPECIAL POSITION. REMARK 375 HOH A4083 LIES ON A SPECIAL POSITION. REMARK 375 HOH A4192 LIES ON A SPECIAL POSITION. REMARK 375 HOH A4217 LIES ON A SPECIAL POSITION. REMARK 375 HOH A4344 LIES ON A SPECIAL POSITION. REMARK 375 HOH A4365 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 MET A 1 REMARK 465 ALA A 2 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 GLU A 115 CG CD OE1 OE2 REMARK 470 ARG A 117 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 134 CG CD OE1 OE2 REMARK 470 LYS A 159 CG CD CE NZ REMARK 470 ARG A 183 CD NE CZ NH1 NH2 REMARK 470 GLU A 306 CG CD OE1 OE2 REMARK 470 GLU A 387 CG CD OE1 OE2 REMARK 470 LYS A 533 CG CD CE NZ REMARK 470 ARG A 596 CG CD NE CZ NH1 NH2 REMARK 470 SER A 701 OG REMARK 470 GLU A 726 CG CD OE1 OE2 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 O1 FOL A 2887 O HOH A 3701 1.87 REMARK 500 O HOH A 3285 O HOH A 3583 1.91 REMARK 500 O HOH A 3270 O HOH A 4248 2.11 REMARK 500 O HOH A 3428 O HOH A 4116 2.15 REMARK 500 OE2 GLU A 735 O HOH A 3598 2.16 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 OE1 GLN A 594 OE1 GLN A 594 3656 1.67 REMARK 500 O HOH A 4282 O HOH A 4282 2565 2.08 REMARK 500 O HOH A 4190 O HOH A 4190 2565 2.13 REMARK 500 REMARK 500 REMARK: NULL 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 827 NE - CZ - NH2 ANGL. DEV. = -5.0 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 ALA A 12 44.31 -106.94 REMARK 500 MET A 41 78.36 -162.89 REMARK 500 ASN A 244 23.25 -140.29 REMARK 500 ALA A 499 -114.79 -136.99 REMARK 500 THR A 704 -59.56 -125.37 REMARK 500 ARG A 755 -26.24 -141.00 REMARK 500 LYS A 761 -6.95 77.97 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 NA A2001 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 257 OD2 REMARK 620 2 VAL A 412 O 173.0 REMARK 620 3 HOH A2944 O 89.8 85.0 REMARK 620 4 HOH A3153 O 91.7 85.1 104.8 REMARK 620 5 HOH A3552 O 82.8 101.3 84.3 169.4 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 2001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FOL A 2887 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FAD A 902 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1PJ5 RELATED DB: PDB REMARK 900 DIMETHYLGLYCINE OXIDASE IN COMPLEX WITH ACETATE REMARK 900 RELATED ID: 1PJ7 RELATED DB: PDB DBREF 1PJ6 A 1 830 UNP Q9AGP8 Q9AGP8_ARTGO 1 830 SEQRES 1 A 830 MET ALA SER THR PRO ARG ILE VAL ILE ILE GLY ALA GLY SEQRES 2 A 830 ILE VAL GLY THR ASN LEU ALA ASP GLU LEU VAL THR ARG SEQRES 3 A 830 GLY TRP ASN ASN ILE THR VAL LEU ASP GLN GLY PRO LEU SEQRES 4 A 830 ASN MET PRO GLY GLY SER THR SER HIS ALA PRO GLY LEU SEQRES 5 A 830 VAL PHE GLN THR ASN PRO SER LYS THR MET ALA SER PHE SEQRES 6 A 830 ALA LYS TYR THR VAL GLU LYS LEU LEU SER LEU THR GLU SEQRES 7 A 830 ASP GLY VAL SER CYS PHE ASN GLN VAL GLY GLY LEU GLU SEQRES 8 A 830 VAL ALA THR THR GLU THR ARG LEU ALA ASP LEU LYS ARG SEQRES 9 A 830 LYS LEU GLY TYR ALA ALA ALA TRP GLY ILE GLU GLY ARG SEQRES 10 A 830 LEU LEU SER PRO ALA GLU CYS GLN GLU LEU TYR PRO LEU SEQRES 11 A 830 LEU ASP GLY GLU ASN ILE LEU GLY GLY LEU HIS VAL PRO SEQRES 12 A 830 SER ASP GLY LEU ALA SER ALA ALA ARG ALA VAL GLN LEU SEQRES 13 A 830 LEU ILE LYS ARG THR GLU SER ALA GLY VAL THR TYR ARG SEQRES 14 A 830 GLY SER THR THR VAL THR GLY ILE GLU GLN SER GLY GLY SEQRES 15 A 830 ARG VAL THR GLY VAL GLN THR ALA ASP GLY VAL ILE PRO SEQRES 16 A 830 ALA ASP ILE VAL VAL SER CYS ALA GLY PHE TRP GLY ALA SEQRES 17 A 830 LYS ILE GLY ALA MET ILE GLY MET ALA VAL PRO LEU LEU SEQRES 18 A 830 PRO LEU ALA HIS GLN TYR VAL LYS THR THR PRO VAL PRO SEQRES 19 A 830 ALA GLN GLN GLY ARG ASN ASP GLN PRO ASN GLY ALA ARG SEQRES 20 A 830 LEU PRO ILE LEU ARG HIS GLN ASP GLN ASP LEU TYR TYR SEQRES 21 A 830 ARG GLU HIS GLY ASP ARG TYR GLY ILE GLY SER TYR ALA SEQRES 22 A 830 HIS ARG PRO MET PRO VAL ASP VAL ASP THR LEU GLY ALA SEQRES 23 A 830 TYR ALA PRO GLU THR VAL SER GLU HIS HIS MET PRO SER SEQRES 24 A 830 ARG LEU ASP PHE THR LEU GLU ASP PHE LEU PRO ALA TRP SEQRES 25 A 830 GLU ALA THR LYS GLN LEU LEU PRO ALA LEU ALA ASP SER SEQRES 26 A 830 GLU ILE GLU ASP GLY PHE ASN GLY ILE PHE SER PHE THR SEQRES 27 A 830 PRO ASP GLY GLY PRO LEU LEU GLY GLU SER LYS GLU LEU SEQRES 28 A 830 ASP GLY PHE TYR VAL ALA GLU ALA VAL TRP VAL THR HIS SEQRES 29 A 830 SER ALA GLY VAL ALA LYS ALA MET ALA GLU LEU LEU THR SEQRES 30 A 830 THR GLY ARG SER GLU THR ASP LEU GLY GLU CYS ASP ILE SEQRES 31 A 830 THR ARG PHE GLU ASP VAL GLN LEU THR PRO GLU TYR VAL SEQRES 32 A 830 SER GLU THR SER GLN GLN ASN PHE VAL GLU ILE TYR ASP SEQRES 33 A 830 VAL LEU HIS PRO LEU GLN PRO ARG LEU SER PRO ARG ASN SEQRES 34 A 830 LEU ARG VAL SER PRO PHE HIS ALA ARG HIS LYS GLU LEU SEQRES 35 A 830 GLY ALA PHE PHE LEU GLU ALA GLY GLY TRP GLU ARG PRO SEQRES 36 A 830 TYR TRP PHE GLU ALA ASN ALA ALA LEU LEU LYS GLU MET SEQRES 37 A 830 PRO ALA GLU TRP LEU PRO PRO ALA ARG ASP ALA TRP SER SEQRES 38 A 830 GLY MET PHE SER SER PRO ILE ALA ALA ALA GLU ALA TRP SEQRES 39 A 830 LYS THR ARG THR ALA VAL ALA MET TYR ASP MET THR PRO SEQRES 40 A 830 LEU LYS ARG LEU GLU VAL SER GLY PRO GLY ALA LEU LYS SEQRES 41 A 830 LEU LEU GLN GLU LEU THR THR ALA ASP LEU ALA LYS LYS SEQRES 42 A 830 PRO GLY ALA VAL THR TYR THR LEU LEU LEU ASP HIS ALA SEQRES 43 A 830 GLY GLY VAL ARG SER ASP ILE THR VAL ALA ARG LEU SER SEQRES 44 A 830 GLU ASP THR PHE GLN LEU GLY ALA ASN GLY ASN ILE ASP SEQRES 45 A 830 THR ALA TYR PHE GLU ARG ALA ALA ARG HIS GLN THR GLN SEQRES 46 A 830 SER GLY SER ALA THR ASP TRP VAL GLN VAL ARG ASP THR SEQRES 47 A 830 THR GLY GLY THR CYS CYS ILE GLY LEU TRP GLY PRO LEU SEQRES 48 A 830 ALA ARG ASP LEU VAL SER LYS VAL SER ASP ASP ASP PHE SEQRES 49 A 830 THR ASN ASP GLY LEU LYS TYR PHE ARG ALA LYS ASN VAL SEQRES 50 A 830 VAL ILE GLY GLY ILE PRO VAL THR ALA MET ARG LEU SER SEQRES 51 A 830 TYR VAL GLY GLU LEU GLY TRP GLU LEU TYR THR SER ALA SEQRES 52 A 830 ASP ASN GLY GLN ARG LEU TRP ASP ALA LEU TRP GLN ALA SEQRES 53 A 830 GLY GLN PRO PHE GLY VAL ILE ALA ALA GLY ARG ALA ALA SEQRES 54 A 830 PHE SER SER LEU ARG LEU GLU LYS GLY TYR ARG SER TRP SEQRES 55 A 830 GLY THR ASP MET THR THR GLU HIS ASP PRO PHE GLU ALA SEQRES 56 A 830 GLY LEU GLY PHE ALA VAL LYS MET ALA LYS GLU SER PHE SEQRES 57 A 830 ILE GLY LYS GLY ALA LEU GLU GLY ARG THR GLU GLU ALA SEQRES 58 A 830 SER ALA ARG ARG LEU ARG CYS LEU THR ILE ASP ASP GLY SEQRES 59 A 830 ARG SER ILE VAL LEU GLY LYS GLU PRO VAL PHE TYR LYS SEQRES 60 A 830 GLU GLN ALA VAL GLY TYR VAL THR SER ALA ALA TYR GLY SEQRES 61 A 830 TYR THR VAL ALA LYS PRO ILE ALA TYR SER TYR LEU PRO SEQRES 62 A 830 GLY THR VAL SER VAL GLY ASP SER VAL ASP ILE GLU TYR SEQRES 63 A 830 PHE GLY ARG ARG ILE THR ALA THR VAL THR GLU ASP PRO SEQRES 64 A 830 LEU TYR ASP PRO LYS MET THR ARG LEU ARG GLY HET NA A2001 1 HET FOL A2887 32 HET FAD A 902 53 HETNAM NA SODIUM ION HETNAM FOL FOLIC ACID HETNAM FAD FLAVIN-ADENINE DINUCLEOTIDE FORMUL 2 NA NA 1+ FORMUL 3 FOL C19 H19 N7 O6 FORMUL 4 FAD C27 H33 N9 O15 P2 FORMUL 5 HOH *1612(H2 O) HELIX 1 1 GLY A 13 ARG A 26 1 14 HELIX 2 2 GLY A 44 ALA A 49 5 6 HELIX 3 3 SER A 59 LEU A 76 1 18 HELIX 4 4 THR A 95 GLY A 113 1 19 HELIX 5 5 SER A 120 TYR A 128 1 9 HELIX 6 6 ASP A 132 ILE A 136 5 5 HELIX 7 7 SER A 149 ALA A 164 1 16 HELIX 8 8 ALA A 203 PHE A 205 5 3 HELIX 9 9 TRP A 206 MET A 213 1 8 HELIX 10 10 VAL A 233 GLN A 237 5 5 HELIX 11 11 GLN A 254 GLN A 256 5 3 HELIX 12 12 ASP A 280 LEU A 284 5 5 HELIX 13 13 ALA A 288 VAL A 292 5 5 HELIX 14 14 THR A 304 LEU A 319 1 16 HELIX 15 15 PRO A 320 SER A 325 5 6 HELIX 16 16 TRP A 361 THR A 363 5 3 HELIX 17 17 HIS A 364 GLY A 379 1 16 HELIX 18 18 ASP A 389 PHE A 393 5 5 HELIX 19 19 GLU A 394 LEU A 398 5 5 HELIX 20 20 THR A 399 GLU A 413 1 15 HELIX 21 21 PHE A 435 LEU A 442 1 8 HELIX 22 22 ALA A 460 MET A 468 5 9 HELIX 23 23 PRO A 469 LEU A 473 5 5 HELIX 24 24 PRO A 487 ALA A 499 1 13 HELIX 25 25 GLY A 517 THR A 526 1 10 HELIX 26 26 GLY A 569 GLY A 587 1 19 HELIX 27 27 LEU A 611 SER A 617 1 7 HELIX 28 28 ASN A 665 GLN A 678 1 14 HELIX 29 29 PRO A 679 GLY A 681 5 3 HELIX 30 30 GLY A 686 LYS A 697 1 12 HELIX 31 31 LEU A 717 VAL A 721 5 5 HELIX 32 32 LYS A 731 GLU A 735 5 5 SHEET 1 A 6 THR A 167 ARG A 169 0 SHEET 2 A 6 ILE A 31 LEU A 34 1 N VAL A 33 O THR A 167 SHEET 3 A 6 ILE A 7 ILE A 10 1 N ILE A 9 O LEU A 34 SHEET 4 A 6 ILE A 198 SER A 201 1 O VAL A 200 N ILE A 10 SHEET 5 A 6 PHE A 354 GLU A 358 1 O TYR A 355 N SER A 201 SHEET 6 A 6 LEU A 344 GLU A 347 -1 N LEU A 344 O GLU A 358 SHEET 1 B 3 LEU A 52 VAL A 53 0 SHEET 2 B 3 GLY A 146 ALA A 148 -1 O GLY A 146 N VAL A 53 SHEET 3 B 3 PHE A 84 ASN A 85 -1 N ASN A 85 O LEU A 147 SHEET 1 C 2 THR A 77 GLU A 78 0 SHEET 2 C 2 VAL A 81 SER A 82 -1 O VAL A 81 N GLU A 78 SHEET 1 D 9 ARG A 117 LEU A 119 0 SHEET 2 D 9 GLY A 138 VAL A 142 -1 O GLY A 139 N LEU A 119 SHEET 3 D 9 GLY A 89 ALA A 93 -1 N GLY A 89 O VAL A 142 SHEET 4 D 9 ILE A 250 HIS A 253 1 O ILE A 250 N LEU A 90 SHEET 5 D 9 LEU A 258 HIS A 263 -1 O LEU A 258 N HIS A 253 SHEET 6 D 9 ARG A 266 SER A 271 -1 O GLY A 268 N ARG A 261 SHEET 7 D 9 LEU A 221 THR A 230 -1 N VAL A 228 O ILE A 269 SHEET 8 D 9 ILE A 327 PHE A 337 -1 O GLY A 333 N HIS A 225 SHEET 9 D 9 ARG A 300 LEU A 301 -1 N LEU A 301 O ASN A 332 SHEET 1 E 3 VAL A 174 SER A 180 0 SHEET 2 E 3 ARG A 183 THR A 189 -1 O THR A 185 N GLU A 178 SHEET 3 E 3 GLY A 192 PRO A 195 -1 O ILE A 194 N VAL A 187 SHEET 1 F 2 ALA A 444 ALA A 449 0 SHEET 2 F 2 TRP A 452 PHE A 458 -1 O TYR A 456 N PHE A 445 SHEET 1 G 6 ALA A 634 ILE A 639 0 SHEET 2 G 6 ILE A 642 MET A 647 -1 O ALA A 646 N LYS A 635 SHEET 3 G 6 GLY A 656 SER A 662 -1 O TYR A 660 N THR A 645 SHEET 4 G 6 THR A 602 TRP A 608 -1 N LEU A 607 O TRP A 657 SHEET 5 G 6 ALA A 501 ASP A 504 -1 N TYR A 503 O GLY A 606 SHEET 6 G 6 ILE A 683 ALA A 685 1 O ILE A 683 N MET A 502 SHEET 1 H 5 VAL A 537 LEU A 543 0 SHEET 2 H 5 VAL A 549 SER A 559 -1 O ILE A 553 N THR A 540 SHEET 3 H 5 THR A 562 ALA A 567 -1 O GLN A 564 N ALA A 556 SHEET 4 H 5 LYS A 509 SER A 514 -1 N LEU A 511 O LEU A 565 SHEET 5 H 5 GLN A 594 ASP A 597 -1 O ARG A 596 N GLU A 512 SHEET 1 I 7 ARG A 744 ILE A 751 0 SHEET 2 I 7 LYS A 785 PRO A 793 -1 O ALA A 788 N LEU A 749 SHEET 3 I 7 GLN A 769 GLY A 780 -1 N GLY A 780 O LYS A 785 SHEET 4 I 7 PRO A 763 TYR A 766 -1 N VAL A 764 O VAL A 771 SHEET 5 I 7 SER A 801 TYR A 806 -1 O ASP A 803 N PHE A 765 SHEET 6 I 7 ARG A 809 THR A 816 -1 O ALA A 813 N VAL A 802 SHEET 7 I 7 ARG A 744 ILE A 751 -1 N CYS A 748 O THR A 816 LINK NE2 HIS A 48 C8M FAD A 902 1555 1555 1.65 LINK OD2 ASP A 257 NA NA A2001 1555 1555 2.28 LINK O VAL A 412 NA NA A2001 1555 1555 2.29 LINK NA NA A2001 O HOH A2944 1555 1555 2.41 LINK NA NA A2001 O HOH A3153 1555 1555 2.49 LINK NA NA A2001 O HOH A3552 1555 1555 2.43 CISPEP 1 GLN A 242 PRO A 243 0 -3.54 CISPEP 2 SER A 426 PRO A 427 0 -5.91 CISPEP 3 ASP A 818 PRO A 819 0 -3.61 SITE 1 AC1 5 ASP A 257 VAL A 412 HOH A2944 HOH A3153 SITE 2 AC1 5 HOH A3552 SITE 1 AC2 18 LEU A 508 TYR A 539 THR A 554 TYR A 631 SITE 2 AC2 18 PHE A 632 LEU A 649 TYR A 651 GLU A 658 SITE 3 AC2 18 TYR A 699 HOH A2971 HOH A2987 HOH A3177 SITE 4 AC2 18 HOH A3240 HOH A3265 HOH A3374 HOH A3674 SITE 5 AC2 18 HOH A3701 HOH A3929 SITE 1 AC3 38 GLY A 11 GLY A 13 ILE A 14 VAL A 15 SITE 2 AC3 38 ASP A 35 GLN A 36 PRO A 42 GLY A 44 SITE 3 AC3 38 SER A 45 THR A 46 HIS A 48 ALA A 49 SITE 4 AC3 38 PRO A 50 GLY A 51 LEU A 52 THR A 172 SITE 5 AC3 38 VAL A 174 CYS A 202 ALA A 203 GLY A 204 SITE 6 AC3 38 TRP A 206 ILE A 210 HIS A 225 TYR A 259 SITE 7 AC3 38 GLY A 333 ILE A 334 VAL A 360 TRP A 361 SITE 8 AC3 38 VAL A 362 THR A 363 HOH A2909 HOH A2911 SITE 9 AC3 38 HOH A2912 HOH A2915 HOH A2945 HOH A2992 SITE 10 AC3 38 HOH A3010 HOH A3143 CRYST1 70.877 222.506 119.304 90.00 90.00 90.00 C 2 2 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 0.014109 0.000000 0.000000 0.00000 SCALE2 0.000000 0.004494 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008382 0.00000