HEADER OXIDOREDUCTASE 27-MAR-13 4BGM TITLE THREE DIMENSIONAL STRUCTURE OF HUMAN GAMMA-BUTYROBETAINE HYDROXYLASE TITLE 2 IN COMPLEX WITH 3-CARBOXY-N-(2-FLUOROETHYL)-N,N-DIMETHYLPROPAN-1- TITLE 3 AMINIUM CHLORIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: GAMMA-BUTYROBETAINE DIOXYGENASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: GAMMA-BUTYROBETAINE HYDROXYLASE, GAMMA-BBH, GAMMA- COMPND 5 BUTYROBETAINE, 2-OXOGLUTARATE DIOXYGENASE; COMPND 6 EC: 1.14.11.1; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: SACCHAROMYCES CEREVISIAE; SOURCE 6 EXPRESSION_SYSTEM_COMMON: BAKER'S YEAST; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 4932; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: AH22 KEYWDS OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR K.TARS,J.LEITANS,A.KAZAKS REVDAT 6 20-DEC-23 4BGM 1 REMARK LINK REVDAT 5 06-FEB-19 4BGM 1 REMARK REVDAT 4 30-JAN-19 4BGM 1 REMARK REVDAT 3 17-JAN-18 4BGM 1 REMARK REVDAT 2 09-APR-14 4BGM 1 JRNL REVDAT 1 12-MAR-14 4BGM 0 JRNL AUTH K.TARS,J.LEITANS,A.KAZAKS,D.ZELENCOVA,E.LIEPINSH,J.KUKA, JRNL AUTH 2 M.MAKRECKA,D.LOLA,V.ANDRIANOVS,D.GUSTINA,S.GRINBERGA, JRNL AUTH 3 E.LIEPINSH,I.KALVINSH,M.DAMBROVA,E.LOZA,O.PUGOVICS JRNL TITL TARGETING CARNITINE BIOSYNTHESIS: DISCOVERY OF NEW JRNL TITL 2 INHIBITORS AGAINST GAMMA-BUTYROBETAINE HYDROXYLASE. JRNL REF J.MED.CHEM. V. 57 2213 2014 JRNL REFN ISSN 0022-2623 JRNL PMID 24571165 JRNL DOI 10.1021/JM401603E REMARK 2 REMARK 2 RESOLUTION. 2.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.7.0029 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) : 45.27 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.4 REMARK 3 NUMBER OF REFLECTIONS : 16864 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) : 0.160 REMARK 3 R VALUE (WORKING SET) : 0.156 REMARK 3 FREE R VALUE : 0.228 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 906 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) : 2.46 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1239 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.85 REMARK 3 BIN R VALUE (WORKING SET) : 0.2310 REMARK 3 BIN FREE R VALUE SET COUNT : 63 REMARK 3 BIN FREE R VALUE : 0.3300 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3119 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 32 REMARK 3 SOLVENT ATOMS : 267 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 36.53 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.69 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.07000 REMARK 3 B22 (A**2) : 0.07000 REMARK 3 B33 (A**2) : -0.24000 REMARK 3 B12 (A**2) : 0.07000 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): 0.399 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.252 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.170 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 7.338 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.957 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.909 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3231 ; 0.011 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 3030 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4373 ; 1.412 ; 1.948 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6966 ; 0.754 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 385 ; 6.089 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 162 ;38.005 ;24.012 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 549 ;14.153 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 20 ;17.002 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 466 ; 0.080 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3651 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 781 ; 0.001 ; 0.020 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL 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 : 1.20 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 4BGM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 27-MAR-13. REMARK 100 THE DEPOSITION ID IS D_1290056317. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 31-MAR-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : MAX II REMARK 200 BEAMLINE : I911-3 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.03911 REMARK 200 MONOCHROMATOR : DOUBLE SI CRYSTAL MONOCHROMATOR REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17821 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 REMARK 200 RESOLUTION RANGE LOW (A) : 45.270 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 200 DATA REDUNDANCY : 3.300 REMARK 200 R MERGE (I) : 0.10000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.4000 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) : 2.53 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.30 REMARK 200 R MERGE FOR SHELL (I) : 0.43000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: PDB ENTRY 3O2G REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.50 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20 % PEG 3350, 1.5 % 1.6 REMARK 280 -DIAMINOHEXANE, 200 MM AMMONIUM CITRATE PH 7.0, 10 MM ZNSO4, 8 REMARK 280 MM N-OXALYLGLYCINE, 4 MM INHIBITOR, PROTEIN 6.5 MG/ML, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 294K, TIME 2-7 DAYS REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H 3 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z REMARK 290 6555 -X,-X+Y,-Z REMARK 290 7555 X+2/3,Y+1/3,Z+1/3 REMARK 290 8555 -Y+2/3,X-Y+1/3,Z+1/3 REMARK 290 9555 -X+Y+2/3,-X+1/3,Z+1/3 REMARK 290 10555 Y+2/3,X+1/3,-Z+1/3 REMARK 290 11555 X-Y+2/3,-Y+1/3,-Z+1/3 REMARK 290 12555 -X+2/3,-X+Y+1/3,-Z+1/3 REMARK 290 13555 X+1/3,Y+2/3,Z+2/3 REMARK 290 14555 -Y+1/3,X-Y+2/3,Z+2/3 REMARK 290 15555 -X+Y+1/3,-X+2/3,Z+2/3 REMARK 290 16555 Y+1/3,X+2/3,-Z+2/3 REMARK 290 17555 X-Y+1/3,-Y+2/3,-Z+2/3 REMARK 290 18555 -X+1/3,-X+Y+2/3,-Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 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 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 53.59100 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 30.94078 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 68.39033 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 53.59100 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 30.94078 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 68.39033 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 53.59100 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 30.94078 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 68.39033 REMARK 290 SMTRY1 10 -0.500000 0.866025 0.000000 53.59100 REMARK 290 SMTRY2 10 0.866025 0.500000 0.000000 30.94078 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 68.39033 REMARK 290 SMTRY1 11 1.000000 0.000000 0.000000 53.59100 REMARK 290 SMTRY2 11 0.000000 -1.000000 0.000000 30.94078 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 68.39033 REMARK 290 SMTRY1 12 -0.500000 -0.866025 0.000000 53.59100 REMARK 290 SMTRY2 12 -0.866025 0.500000 0.000000 30.94078 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 68.39033 REMARK 290 SMTRY1 13 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 61.88156 REMARK 290 SMTRY3 13 0.000000 0.000000 1.000000 136.78067 REMARK 290 SMTRY1 14 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 14 0.866025 -0.500000 0.000000 61.88156 REMARK 290 SMTRY3 14 0.000000 0.000000 1.000000 136.78067 REMARK 290 SMTRY1 15 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 15 -0.866025 -0.500000 0.000000 61.88156 REMARK 290 SMTRY3 15 0.000000 0.000000 1.000000 136.78067 REMARK 290 SMTRY1 16 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 16 0.866025 0.500000 0.000000 61.88156 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 136.78067 REMARK 290 SMTRY1 17 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 17 0.000000 -1.000000 0.000000 61.88156 REMARK 290 SMTRY3 17 0.000000 0.000000 -1.000000 136.78067 REMARK 290 SMTRY1 18 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 18 -0.866025 0.500000 0.000000 61.88156 REMARK 290 SMTRY3 18 0.000000 0.000000 -1.000000 136.78067 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: 8790 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 30920 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -117.2 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 -0.500000 0.866025 0.000000 0.00000 REMARK 350 BIOMT2 2 0.866025 0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 205.17100 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 C4 16D A 404 LIES ON A SPECIAL POSITION. REMARK 375 HOH A2049 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 ASN A 385 REMARK 465 GLY A 386 REMARK 465 ASN A 387 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 MET A 1 CG SD CE REMARK 470 LYS A 72 CG CD CE NZ REMARK 470 LYS A 167 CG CD CE NZ REMARK 470 LYS A 324 CG CD CE NZ 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 GLU A 24 -15.82 88.86 REMARK 500 LYS A 49 57.79 39.04 REMARK 500 ASP A 70 -158.70 -127.69 REMARK 500 GLU A 81 1.85 84.15 REMARK 500 ASP A 157 45.47 -104.75 REMARK 500 TYR A 194 47.50 -92.76 REMARK 500 HIS A 210 79.72 -117.90 REMARK 500 ASP A 261 112.21 -161.36 REMARK 500 ASP A 265 -105.55 -144.81 REMARK 500 PHE A 291 106.88 -160.39 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 ZN A 403 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 38 SG REMARK 620 2 CYS A 40 SG 113.1 REMARK 620 3 CYS A 43 SG 121.5 108.1 REMARK 620 4 HIS A 82 NE2 110.3 106.4 95.3 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 402 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 202 NE2 REMARK 620 2 ASP A 204 OD1 89.6 REMARK 620 3 HIS A 347 NE2 93.9 94.3 REMARK 620 4 OGA A 400 O1 108.3 100.5 153.2 REMARK 620 5 OGA A 400 O2' 95.5 174.0 82.4 80.7 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 OGA A 400 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DLT A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 16D A 404 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4BG1 RELATED DB: PDB REMARK 900 THREE DIMENSIONAL STRUCTURE OF HUMAN GAMMA-BUTYROBETAINE REMARK 900 HYDROXYLASE IN COMPLEX WITH 1-(3-CARBOXYPROPYL)-1- METHYLPYRROLIDIN- REMARK 900 1-IUM CHLORIDE REMARK 900 RELATED ID: 4BGK RELATED DB: PDB REMARK 900 THREE DIMENSIONAL STRUCTURE OF HUMAN GAMMA-BUTYROBETAINE REMARK 900 HYDROXYLASE IN COMPLEX WITH (3-(TRIMETHYLAMMONIO)PROPYL) PHOSPHINATE REMARK 900 RELATED ID: 4BHF RELATED DB: PDB REMARK 900 THREE DIMENSIONAL STRUCTURE OF HUMAN GAMMA-BUTYROBETAINE REMARK 900 HYDROXYLASE IN COMPLEX WITH 4-(TRIMETHYLAMMONIO)PENTANOATE REMARK 900 RELATED ID: 4BHI RELATED DB: PDB REMARK 900 THREE DIMENSIONAL STRUCTURE OF HUMAN GAMMA-BUTYROBETAINE REMARK 900 HYDROXYLASE IN COMPLEX WITH 3-(1,1,1,2- TETRAMETHYLHYDRAZIN-1-IUM-2- REMARK 900 YL)PROPANOATE REMARK 900 RELATED ID: 4C5W RELATED DB: PDB REMARK 900 THREE DIMENSIONAL STRUCTURE OF HUMAN GAMMA-BUTYROBETAINE REMARK 900 HYDROXYLASE IN COMPLEX WITH 4-(ETHYLDIMETHYLAMMONIO) BUTANOATE DBREF 4BGM A 1 387 UNP O75936 BODG_HUMAN 1 387 SEQRES 1 A 387 MET ALA CYS THR ILE GLN LYS ALA GLU ALA LEU ASP GLY SEQRES 2 A 387 ALA HIS LEU MET GLN ILE LEU TRP TYR ASP GLU GLU GLU SEQRES 3 A 387 SER LEU TYR PRO ALA VAL TRP LEU ARG ASP ASN CYS PRO SEQRES 4 A 387 CYS SER ASP CYS TYR LEU ASP SER ALA LYS ALA ARG LYS SEQRES 5 A 387 LEU LEU VAL GLU ALA LEU ASP VAL ASN ILE GLY ILE LYS SEQRES 6 A 387 GLY LEU ILE PHE ASP ARG LYS LYS VAL TYR ILE THR TRP SEQRES 7 A 387 PRO ASP GLU HIS TYR SER GLU PHE GLN ALA ASP TRP LEU SEQRES 8 A 387 LYS LYS ARG CYS PHE SER LYS GLN ALA ARG ALA LYS LEU SEQRES 9 A 387 GLN ARG GLU LEU PHE PHE PRO GLU CYS GLN TYR TRP GLY SEQRES 10 A 387 SER GLU LEU GLN LEU PRO THR LEU ASP PHE GLU ASP VAL SEQRES 11 A 387 LEU ARG TYR ASP GLU HIS ALA TYR LYS TRP LEU SER THR SEQRES 12 A 387 LEU LYS LYS VAL GLY ILE VAL ARG LEU THR GLY ALA SER SEQRES 13 A 387 ASP LYS PRO GLY GLU VAL SER LYS LEU GLY LYS ARG MET SEQRES 14 A 387 GLY PHE LEU TYR LEU THR PHE TYR GLY HIS THR TRP GLN SEQRES 15 A 387 VAL GLN ASP LYS ILE ASP ALA ASN ASN VAL ALA TYR THR SEQRES 16 A 387 THR GLY LYS LEU SER PHE HIS THR ASP TYR PRO ALA LEU SEQRES 17 A 387 HIS HIS PRO PRO GLY VAL GLN LEU LEU HIS CYS ILE LYS SEQRES 18 A 387 GLN THR VAL THR GLY GLY ASP SER GLU ILE VAL ASP GLY SEQRES 19 A 387 PHE ASN VAL CYS GLN LYS LEU LYS LYS ASN ASN PRO GLN SEQRES 20 A 387 ALA PHE GLN ILE LEU SER SER THR PHE VAL ASP PHE THR SEQRES 21 A 387 ASP ILE GLY VAL ASP TYR CYS ASP PHE SER VAL GLN SER SEQRES 22 A 387 LYS HIS LYS ILE ILE GLU LEU ASP ASP LYS GLY GLN VAL SEQRES 23 A 387 VAL ARG ILE ASN PHE ASN ASN ALA THR ARG ASP THR ILE SEQRES 24 A 387 PHE ASP VAL PRO VAL GLU ARG VAL GLN PRO PHE TYR ALA SEQRES 25 A 387 ALA LEU LYS GLU PHE VAL ASP LEU MET ASN SER LYS GLU SEQRES 26 A 387 SER LYS PHE THR PHE LYS MET ASN PRO GLY ASP VAL ILE SEQRES 27 A 387 THR PHE ASP ASN TRP ARG LEU LEU HIS GLY ARG ARG SER SEQRES 28 A 387 TYR GLU ALA GLY THR GLU ILE SER ARG HIS LEU GLU GLY SEQRES 29 A 387 ALA TYR ALA ASP TRP ASP VAL VAL MET SER ARG LEU ARG SEQRES 30 A 387 ILE LEU ARG GLN ARG VAL GLU ASN GLY ASN HET OGA A 400 10 HET DLT A 401 12 HET ZN A 402 1 HET ZN A 403 1 HET 16D A 404 8 HETNAM OGA N-OXALYLGLYCINE HETNAM DLT 3-CARBOXY-N-(2-FLUOROETHYL)-N,N-DIMETHYLPROPAN-1- HETNAM 2 DLT AMINIUM HETNAM ZN ZINC ION HETNAM 16D HEXANE-1,6-DIAMINE HETSYN 16D 1,6-DIAMINOHEXANE FORMUL 2 OGA C4 H5 N O5 FORMUL 3 DLT C8 H17 F N O2 1+ FORMUL 4 ZN 2(ZN 2+) FORMUL 6 16D C6 H16 N2 FORMUL 7 HOH *267(H2 O) HELIX 1 1 ALA A 31 ASN A 37 1 7 HELIX 2 2 LEU A 54 LEU A 58 5 5 HELIX 3 3 ALA A 88 ARG A 94 1 7 HELIX 4 4 SER A 97 PHE A 110 1 14 HELIX 5 5 PHE A 127 TYR A 133 1 7 HELIX 6 6 TYR A 133 GLY A 148 1 16 HELIX 7 7 GLY A 160 GLY A 170 1 11 HELIX 8 8 ASN A 191 THR A 195 5 5 HELIX 9 9 GLY A 234 ASN A 245 1 12 HELIX 10 10 ASN A 245 SER A 253 1 9 HELIX 11 11 PRO A 303 GLU A 305 5 3 HELIX 12 12 ARG A 306 SER A 323 1 18 HELIX 13 13 ASP A 368 GLU A 384 1 17 SHEET 1 AA 3 ILE A 5 LEU A 11 0 SHEET 2 AA 3 LEU A 16 TRP A 21 -1 O LEU A 16 N LEU A 11 SHEET 3 AA 3 GLU A 26 PRO A 30 -1 O SER A 27 N ILE A 19 SHEET 1 AB 2 TYR A 44 LEU A 45 0 SHEET 2 AB 2 ALA A 50 ARG A 51 -1 O ALA A 50 N LEU A 45 SHEET 1 AC 3 GLY A 66 PHE A 69 0 SHEET 2 AC 3 LYS A 73 THR A 77 -1 O TYR A 75 N ILE A 68 SHEET 3 AC 3 TYR A 83 GLN A 87 -1 O SER A 84 N ILE A 76 SHEET 1 AD 6 THR A 124 ASP A 126 0 SHEET 2 AD 6 ILE A 149 THR A 153 1 O ARG A 151 N LEU A 125 SHEET 3 AD 6 VAL A 337 ASP A 341 -1 O VAL A 337 N LEU A 152 SHEET 4 AD 6 VAL A 214 LYS A 221 -1 O GLN A 215 N PHE A 340 SHEET 5 AD 6 HIS A 361 ALA A 367 -1 O HIS A 361 N LYS A 221 SHEET 6 AD 6 TRP A 181 VAL A 183 -1 O TRP A 181 N GLY A 364 SHEET 1 AE 4 LEU A 199 HIS A 202 0 SHEET 2 AE 4 LEU A 345 ARG A 349 -1 O HIS A 347 N HIS A 202 SHEET 3 AE 4 SER A 229 ASP A 233 -1 O GLU A 230 N GLY A 348 SHEET 4 AE 4 PHE A 328 PHE A 330 -1 O PHE A 328 N ILE A 231 SHEET 1 AF 2 PHE A 256 VAL A 264 0 SHEET 2 AF 2 ASP A 268 LYS A 276 -1 O PHE A 269 N GLY A 263 SHEET 1 AG 2 ILE A 278 LEU A 280 0 SHEET 2 AG 2 VAL A 286 ILE A 289 -1 N VAL A 287 O GLU A 279 LINK SG CYS A 38 ZN ZN A 403 1555 1555 2.28 LINK SG CYS A 40 ZN ZN A 403 1555 1555 2.25 LINK SG CYS A 43 ZN ZN A 403 1555 1555 2.42 LINK NE2 HIS A 82 ZN ZN A 403 1555 1555 2.13 LINK NE2 HIS A 202 ZN ZN A 402 1555 1555 2.25 LINK OD1 ASP A 204 ZN ZN A 402 1555 1555 2.07 LINK NE2 HIS A 347 ZN ZN A 402 1555 1555 2.13 LINK O1 OGA A 400 ZN ZN A 402 1555 1555 1.90 LINK O2' OGA A 400 ZN ZN A 402 1555 1555 2.25 SITE 1 AC1 11 VAL A 183 ALA A 193 HIS A 202 ASP A 204 SITE 2 AC1 11 HIS A 347 ARG A 349 ARG A 360 LEU A 362 SITE 3 AC1 11 DLT A 401 ZN A 402 HOH A2190 SITE 1 AC2 14 TYR A 177 TRP A 181 ASN A 191 ALA A 193 SITE 2 AC2 14 TYR A 194 ASP A 204 TYR A 205 PRO A 206 SITE 3 AC2 14 ASN A 292 THR A 295 TYR A 366 OGA A 400 SITE 4 AC2 14 HOH A2174 HOH A2215 SITE 1 AC3 4 HIS A 202 ASP A 204 HIS A 347 OGA A 400 SITE 1 AC4 4 CYS A 38 CYS A 40 CYS A 43 HIS A 82 SITE 1 AC5 2 TYR A 75 TYR A 83 CRYST1 107.182 107.182 205.171 90.00 90.00 120.00 H 3 2 18 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 0.009330 0.005387 0.000000 0.00000 SCALE2 0.000000 0.010773 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004874 0.00000