PDB Short entry for 4D50 HEADER OXIDOREDUCTASE 31-OCT-14 4D50 TITLE STRUCTURE OF HUMAN DEOXYHYPUSINE HYDROXYLASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: DEOXYHYPUSINE HYDROXYLASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: HDOHH, DEOXYHYPUSINE DIOXYGENASE, DEOXYHYPUSINE COMPND 5 MONOOXYGENASE, HEAT-LIKE REPEAT-CONTAINING PROTEIN 1; COMPND 6 EC: 1.14.99.29; 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: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PGEX-6P-1 KEYWDS OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR Z.HAN,N.SAKAI,R.HILGENFELD REVDAT 3 27-MAY-15 4D50 1 JRNL REVDAT 2 22-APR-15 4D50 1 JRNL REVDAT 1 15-APR-15 4D50 0 JRNL AUTH Z.HAN,N.SAKAI,L.H.BOTTGER,S.KLINKE,J.HAUBER,A.X.TRAUTWEIN, JRNL AUTH 2 R.HILGENFELD JRNL TITL CRYSTAL STRUCTURE OF THE PEROXO-DIIRON(III) INTERMEDIATE OF JRNL TITL 2 DEOXYHYPUSINE HYDROXYLASE, AN OXYGENASE INVOLVED IN JRNL TITL 3 HYPUSINATION. JRNL REF STRUCTURE V. 23 882 2015 JRNL REFN ISSN 0969-2126 JRNL PMID 25865244 JRNL DOI 10.1016/J.STR.2015.03.002 REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.7.0029 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU, REMARK 3 STEINER,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) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.85 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 95.94 REMARK 3 NUMBER OF REFLECTIONS : 54485 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) : 0.20481 REMARK 3 R VALUE (WORKING SET) : 0.20261 REMARK 3 FREE R VALUE : 0.24650 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.1 REMARK 3 FREE R VALUE TEST SET COUNT : 2912 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) : 1.700 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.744 REMARK 3 REFLECTION IN BIN (WORKING SET) : 4093 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.65 REMARK 3 BIN R VALUE (WORKING SET) : 0.255 REMARK 3 BIN FREE R VALUE SET COUNT : 227 REMARK 3 BIN FREE R VALUE : 0.320 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4410 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 28 REMARK 3 SOLVENT ATOMS : 440 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 14.9 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.899 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.00 REMARK 3 B22 (A**2) : 0.00 REMARK 3 B33 (A**2) : 0.00 REMARK 3 B12 (A**2) : 0.00 REMARK 3 B13 (A**2) : 0.00 REMARK 3 B23 (A**2) : 0.00 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.133 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.130 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.092 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.787 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.941 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.915 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4532 ; 0.018 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 4337 ; 0.006 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6149 ; 1.769 ; 1.981 REMARK 3 BOND ANGLES OTHERS (DEGREES): 9944 ; 1.189 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 584 ; 4.776 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 218 ;34.605 ;24.037 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 732 ;15.327 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 42 ;17.808 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 679 ; 0.111 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5270 ; 0.011 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 1037 ; 0.005 ; 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): 1 ;46.413 ; 5.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 16 ;31.558 ; 5.000 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. REMARK 4 REMARK 4 4D50 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 01-NOV-14. REMARK 100 THE PDBE ID CODE IS EBI-62185. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-MAY-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.2 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : BESSY REMARK 200 BEAMLINE : 14.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.91841 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : AUTOPROC REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 57441 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.70 REMARK 200 RESOLUTION RANGE LOW (A) : 20.00 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 4.3 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.0 REMARK 200 DATA REDUNDANCY : 3.4 REMARK 200 R MERGE (I) : 0.05 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 14.00 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.79 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.7 REMARK 200 DATA REDUNDANCY IN SHELL : 3.5 REMARK 200 R MERGE FOR SHELL (I) : 0.24 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 4.30 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: NONE REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.14 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30% POLYETHYLENE GLYCOL 6000 (W/V), REMARK 280 100 MM BIS-TRIS PROPANE PH 7.2 - 7.4, 400 MM GUANIDINE CHLORIDE REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 24.31800 REMARK 290 SMTRY3 2 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 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 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PQS REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 ARG A 286 REMARK 465 ALA A 287 REMARK 465 PHE A 288 REMARK 465 GLN A 289 REMARK 465 ARG B 286 REMARK 465 ALA B 287 REMARK 465 PHE B 288 REMARK 465 GLN B 289 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 O PRO A -4 O HOH A 2001 2.03 REMARK 500 OE1 GLU A 57 O HOH A 2053 1.84 REMARK 500 OE2 GLU A 244 O HOH A 2053 1.90 REMARK 500 CG MET A 279 O HOH A 2245 2.06 REMARK 500 OH TYR A 280 O HOH A 2246 2.16 REMARK 500 C SER B -1 N MET B 1 1.60 REMARK 500 OE2 GLU B 105 O HOH B 2070 2.01 REMARK 500 OE1 GLN B 217 O HOH B 2144 1.98 REMARK 500 O HOH A 2022 O HOH A 2023 2.07 REMARK 500 O HOH A 2035 O HOH A 2108 1.92 REMARK 500 O HOH A 2040 O HOH A 2130 2.18 REMARK 500 O HOH A 2086 O HOH A 2239 2.20 REMARK 500 O HOH A 2094 O HOH A 2123 2.09 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 SER A -1 C MET A 1 N 0.214 REMARK 500 SER B -1 C MET B 1 N 0.276 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 SER A -1 O - C - N ANGL. DEV. = -15.0 DEGREES REMARK 500 ARG A 183 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 ARG A 239 NE - CZ - NH2 ANGL. DEV. = -4.1 DEGREES REMARK 500 SER B -1 O - C - N ANGL. DEV. = -14.0 DEGREES REMARK 500 ARG B 183 NE - CZ - NH2 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 PHE A 47 -6.55 -59.44 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 SER A -1 -20.64 REMARK 500 SER B -1 -19.03 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 FE A 301 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 90 OE1 REMARK 620 2 HIS A 207 NE2 174.6 REMARK 620 3 PER A 303 O2 92.5 90.8 REMARK 620 4 HOH A2003 O 85.3 99.4 82.4 REMARK 620 5 HIS A 89 NE2 84.4 90.6 103.0 168.6 REMARK 620 6 HOH A2001 O 90.4 87.4 166.9 85.2 89.9 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 FE B 301 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 PER B 303 O2 REMARK 620 2 HOH B2003 O 76.9 REMARK 620 3 HIS B 207 NE2 81.1 96.0 REMARK 620 4 HIS B 89 NE2 105.5 170.8 93.2 REMARK 620 5 GLU B 90 OE1 100.7 87.5 176.4 83.3 REMARK 620 6 HOH B2001 O 145.6 73.6 84.8 106.4 95.3 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 FE A 302 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 56 NE2 REMARK 620 2 HIS A 240 NE2 92.3 REMARK 620 3 GLU A 241 OE1 173.0 89.3 REMARK 620 4 PER A 303 O1 97.3 87.6 89.6 REMARK 620 5 PER A 303 O2 83.0 118.5 102.3 33.7 REMARK 620 6 HOH A2003 O 95.6 170.7 82.3 96.1 67.4 REMARK 620 7 HOH A2002 O 87.8 92.1 85.4 174.9 148.2 83.4 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 FE B 302 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU B 241 OE1 REMARK 620 2 HIS B 56 NE2 168.2 REMARK 620 3 HIS B 240 NE2 82.5 93.9 REMARK 620 4 PER B 303 O1 94.6 96.2 83.7 REMARK 620 5 PER B 303 O2 101.7 89.9 119.0 35.4 REMARK 620 6 HOH B2003 O 87.6 94.8 169.0 102.1 67.9 REMARK 620 7 HOH B2002 O 84.9 84.4 97.5 178.6 143.4 76.6 REMARK 620 N 1 2 3 4 5 6 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FE A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FE A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PER A 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GAI A 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GAI A 405 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GAI A 406 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GAI A 407 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FE B 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FE B 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PER B 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GAI B 404 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4D4Z RELATED DB: PDB REMARK 900 STRUCTURE OF HUMAN DEOXYHYPUSINE HYDROXYLASE IN COMPLEX REMARK 900 WITH GLYCEROL REMARK 999 REMARK 999 SEQUENCE REMARK 999 FIVE RESIDUES (GPLGS) IN N-TERMINUS ARE FROM EXPRESSION REMARK 999 VECTOR. DBREF 4D50 A 1 289 UNP Q9BU89 DOHH_HUMAN 1 289 DBREF 4D50 B 1 289 UNP Q9BU89 DOHH_HUMAN 1 289 SEQADV 4D50 GLY A -5 UNP Q9BU89 EXPRESSION TAG SEQADV 4D50 PRO A -4 UNP Q9BU89 EXPRESSION TAG SEQADV 4D50 LEU A -3 UNP Q9BU89 EXPRESSION TAG SEQADV 4D50 GLY A -2 UNP Q9BU89 EXPRESSION TAG SEQADV 4D50 SER A -1 UNP Q9BU89 EXPRESSION TAG SEQADV 4D50 GLY B -5 UNP Q9BU89 EXPRESSION TAG SEQADV 4D50 PRO B -4 UNP Q9BU89 EXPRESSION TAG SEQADV 4D50 LEU B -3 UNP Q9BU89 EXPRESSION TAG SEQADV 4D50 GLY B -2 UNP Q9BU89 EXPRESSION TAG SEQADV 4D50 SER B -1 UNP Q9BU89 EXPRESSION TAG SEQRES 1 A 294 GLY PRO LEU GLY SER MET VAL THR GLU GLN GLU VAL ASP SEQRES 2 A 294 ALA ILE GLY GLN THR LEU VAL ASP PRO LYS GLN PRO LEU SEQRES 3 A 294 GLN ALA ARG PHE ARG ALA LEU PHE THR LEU ARG GLY LEU SEQRES 4 A 294 GLY GLY PRO GLY ALA ILE ALA TRP ILE SER GLN ALA PHE SEQRES 5 A 294 ASP ASP ASP SER ALA LEU LEU LYS HIS GLU LEU ALA TYR SEQRES 6 A 294 CYS LEU GLY GLN MET GLN ASP ALA ARG ALA ILE PRO MET SEQRES 7 A 294 LEU VAL ASP VAL LEU GLN ASP THR ARG GLN GLU PRO MET SEQRES 8 A 294 VAL ARG HIS GLU ALA GLY GLU ALA LEU GLY ALA ILE GLY SEQRES 9 A 294 ASP PRO GLU VAL LEU GLU ILE LEU LYS GLN TYR SER SER SEQRES 10 A 294 ASP PRO VAL ILE GLU VAL ALA GLU THR CYS GLN LEU ALA SEQRES 11 A 294 VAL ARG ARG LEU GLU TRP LEU GLN GLN HIS GLY GLY GLU SEQRES 12 A 294 PRO ALA ALA GLY PRO TYR LEU SER VAL ASP PRO ALA PRO SEQRES 13 A 294 PRO ALA GLU GLU ARG ASP VAL GLY ARG LEU ARG GLU ALA SEQRES 14 A 294 LEU LEU ASP GLU SER ARG PRO LEU PHE GLU ARG TYR ARG SEQRES 15 A 294 ALA MET PHE ALA LEU ARG ASN ALA GLY GLY GLU GLU ALA SEQRES 16 A 294 ALA LEU ALA LEU ALA GLU GLY LEU HIS CYS GLY SER ALA SEQRES 17 A 294 LEU PHE ARG HIS GLU VAL GLY TYR VAL LEU GLY GLN LEU SEQRES 18 A 294 GLN HIS GLU ALA ALA VAL PRO GLN LEU ALA ALA ALA LEU SEQRES 19 A 294 ALA ARG CYS THR GLU ASN PRO MET VAL ARG HIS GLU CYS SEQRES 20 A 294 ALA GLU ALA LEU GLY ALA ILE ALA ARG PRO ALA CYS LEU SEQRES 21 A 294 ALA ALA LEU GLN ALA HIS ALA ASP ASP PRO GLU ARG VAL SEQRES 22 A 294 VAL ARG GLU SER CYS GLU VAL ALA LEU ASP MET TYR GLU SEQRES 23 A 294 HIS GLU THR GLY ARG ALA PHE GLN SEQRES 1 B 294 GLY PRO LEU GLY SER MET VAL THR GLU GLN GLU VAL ASP SEQRES 2 B 294 ALA ILE GLY GLN THR LEU VAL ASP PRO LYS GLN PRO LEU SEQRES 3 B 294 GLN ALA ARG PHE ARG ALA LEU PHE THR LEU ARG GLY LEU SEQRES 4 B 294 GLY GLY PRO GLY ALA ILE ALA TRP ILE SER GLN ALA PHE SEQRES 5 B 294 ASP ASP ASP SER ALA LEU LEU LYS HIS GLU LEU ALA TYR SEQRES 6 B 294 CYS LEU GLY GLN MET GLN ASP ALA ARG ALA ILE PRO MET SEQRES 7 B 294 LEU VAL ASP VAL LEU GLN ASP THR ARG GLN GLU PRO MET SEQRES 8 B 294 VAL ARG HIS GLU ALA GLY GLU ALA LEU GLY ALA ILE GLY SEQRES 9 B 294 ASP PRO GLU VAL LEU GLU ILE LEU LYS GLN TYR SER SER SEQRES 10 B 294 ASP PRO VAL ILE GLU VAL ALA GLU THR CYS GLN LEU ALA SEQRES 11 B 294 VAL ARG ARG LEU GLU TRP LEU GLN GLN HIS GLY GLY GLU SEQRES 12 B 294 PRO ALA ALA GLY PRO TYR LEU SER VAL ASP PRO ALA PRO SEQRES 13 B 294 PRO ALA GLU GLU ARG ASP VAL GLY ARG LEU ARG GLU ALA SEQRES 14 B 294 LEU LEU ASP GLU SER ARG PRO LEU PHE GLU ARG TYR ARG SEQRES 15 B 294 ALA MET PHE ALA LEU ARG ASN ALA GLY GLY GLU GLU ALA SEQRES 16 B 294 ALA LEU ALA LEU ALA GLU GLY LEU HIS CYS GLY SER ALA SEQRES 17 B 294 LEU PHE ARG HIS GLU VAL GLY TYR VAL LEU GLY GLN LEU SEQRES 18 B 294 GLN HIS GLU ALA ALA VAL PRO GLN LEU ALA ALA ALA LEU SEQRES 19 B 294 ALA ARG CYS THR GLU ASN PRO MET VAL ARG HIS GLU CYS SEQRES 20 B 294 ALA GLU ALA LEU GLY ALA ILE ALA ARG PRO ALA CYS LEU SEQRES 21 B 294 ALA ALA LEU GLN ALA HIS ALA ASP ASP PRO GLU ARG VAL SEQRES 22 B 294 VAL ARG GLU SER CYS GLU VAL ALA LEU ASP MET TYR GLU SEQRES 23 B 294 HIS GLU THR GLY ARG ALA PHE GLN HET FE A 301 1 HET FE A 302 1 HET PER A 303 2 HET GAI A 404 4 HET GAI A 405 4 HET GAI A 406 4 HET GAI A 407 4 HET FE B 301 1 HET FE B 302 1 HET PER B 303 2 HET GAI B 404 4 HETNAM FE FE (III) ION HETNAM GAI GUANIDINE HETNAM PER PEROXIDE ION FORMUL 3 FE 4(FE 3+) FORMUL 4 GAI 5(C H5 N3) FORMUL 5 PER 2(O2 2-) FORMUL 6 HOH *440(H2 O) HELIX 1 1 PRO A -4 ASP A 16 1 20 HELIX 2 2 PRO A 20 GLY A 35 1 16 HELIX 3 3 GLY A 36 ALA A 46 1 11 HELIX 4 4 PHE A 47 ASP A 49 5 3 HELIX 5 5 SER A 51 GLN A 66 1 16 HELIX 6 6 ASP A 67 ARG A 69 5 3 HELIX 7 7 ALA A 70 ASP A 80 1 11 HELIX 8 8 GLU A 84 GLY A 99 1 16 HELIX 9 9 ASP A 100 GLU A 102 5 3 HELIX 10 10 VAL A 103 SER A 111 1 9 HELIX 11 11 VAL A 115 GLY A 136 1 22 HELIX 12 12 ASP A 157 ASP A 167 1 11 HELIX 13 13 PRO A 171 GLY A 186 1 16 HELIX 14 14 GLY A 187 GLY A 197 1 11 HELIX 15 15 LEU A 198 CYS A 200 5 3 HELIX 16 16 SER A 202 GLN A 217 1 16 HELIX 17 17 HIS A 218 ALA A 220 5 3 HELIX 18 18 ALA A 221 ARG A 231 1 11 HELIX 19 19 ASN A 235 ALA A 250 1 16 HELIX 20 20 ARG A 251 HIS A 261 1 11 HELIX 21 21 GLU A 266 GLY A 285 1 20 HELIX 22 22 PRO B -4 ASP B 16 1 20 HELIX 23 23 PRO B 20 GLY B 35 1 16 HELIX 24 24 GLY B 36 ALA B 46 1 11 HELIX 25 25 PHE B 47 ASP B 49 5 3 HELIX 26 26 SER B 51 GLN B 66 1 16 HELIX 27 27 ASP B 67 ARG B 69 5 3 HELIX 28 28 ALA B 70 ASP B 80 1 11 HELIX 29 29 GLU B 84 GLY B 99 1 16 HELIX 30 30 ASP B 100 GLU B 102 5 3 HELIX 31 31 VAL B 103 TYR B 110 1 8 HELIX 32 32 SER B 111 ASP B 113 5 3 HELIX 33 33 VAL B 115 GLY B 136 1 22 HELIX 34 34 ASP B 157 LEU B 166 1 10 HELIX 35 35 PRO B 171 GLY B 186 1 16 HELIX 36 36 GLY B 186 GLY B 197 1 12 HELIX 37 37 LEU B 198 CYS B 200 5 3 HELIX 38 38 SER B 202 GLN B 217 1 16 HELIX 39 39 HIS B 218 ALA B 220 5 3 HELIX 40 40 ALA B 221 ARG B 231 1 11 HELIX 41 41 ASN B 235 ALA B 250 1 16 HELIX 42 42 ARG B 251 ALA B 262 1 12 HELIX 43 43 GLU B 266 GLY B 285 1 20 LINK FE FE A 301 OE1 GLU A 90 1555 1555 2.06 LINK FE FE A 301 NE2 HIS A 207 1555 1555 2.27 LINK FE FE A 301 O1 PER A 303 1555 1555 2.23 LINK FE FE A 301 O HOH A2003 1555 1555 2.14 LINK FE FE A 301 NE2 HIS A 89 1555 1555 2.24 LINK FE FE A 301 O HOH A2001 1555 1555 2.18 LINK FE FE A 302 NE2 HIS A 56 1555 1555 2.33 LINK FE FE A 302 NE2 HIS A 240 1555 1555 2.20 LINK FE FE A 302 O HOH A2002 1555 1555 2.16 LINK FE FE A 302 O HOH A2003 1555 1555 2.38 LINK FE FE A 302 O2 PER A 303 1555 1555 2.18 LINK FE FE A 302 OE1 GLU A 241 1555 1555 2.10 LINK FE FE B 301 O1 PER B 303 1555 1555 2.21 LINK FE FE B 301 O HOH B2001 1555 1555 2.12 LINK FE FE B 301 OE1 GLU B 90 1555 1555 2.10 LINK FE FE B 301 NE2 HIS B 89 1555 1555 2.23 LINK FE FE B 301 NE2 HIS B 207 1555 1555 2.23 LINK FE FE B 301 O HOH B2003 1555 1555 2.15 LINK FE FE B 302 NE2 HIS B 56 1555 1555 2.34 LINK FE FE B 302 NE2 HIS B 240 1555 1555 2.29 LINK FE FE B 302 O2 PER B 303 1555 1555 2.17 LINK FE FE B 302 O HOH B2003 1555 1555 2.19 LINK FE FE B 302 O HOH B2002 1555 1555 2.18 LINK FE FE B 302 OE1 GLU B 241 1555 1555 1.99 SITE 1 AC1 6 HIS A 89 GLU A 90 HIS A 207 PER A 303 SITE 2 AC1 6 HOH A2001 HOH A2003 SITE 1 AC2 6 HIS A 56 HIS A 240 GLU A 241 PER A 303 SITE 2 AC2 6 HOH A2002 HOH A2003 SITE 1 AC3 10 HIS A 56 HIS A 89 GLU A 90 HIS A 207 SITE 2 AC3 10 MET A 237 HIS A 240 GLU A 241 FE A 301 SITE 3 AC3 10 FE A 302 HOH A2003 SITE 1 AC4 4 GLU A 274 LEU A 277 ASP A 278 HOH A2227 SITE 1 AC5 4 GLU A 4 PRO A 37 GLU A 188 LEU B 145 SITE 1 AC6 3 THR A 233 GLU A 234 HOH A2255 SITE 1 AC7 6 GLY A 36 PRO A 37 ILE A 40 ASP A 67 SITE 2 AC7 6 ARG A 69 HOH A2060 SITE 1 AC8 7 HIS B 89 GLU B 90 HIS B 207 FE B 302 SITE 2 AC8 7 PER B 303 HOH B2001 HOH B2003 SITE 1 AC9 7 HIS B 56 HIS B 240 GLU B 241 FE B 301 SITE 2 AC9 7 PER B 303 HOH B2002 HOH B2003 SITE 1 BC1 11 HIS B 56 MET B 86 HIS B 89 GLU B 90 SITE 2 BC1 11 HIS B 207 MET B 237 HIS B 240 GLU B 241 SITE 3 BC1 11 FE B 301 FE B 302 HOH B2003 SITE 1 BC2 6 LEU A 145 GLU B 4 GLY B 36 PRO B 37 SITE 2 BC2 6 GLU B 188 HOH B2025 CRYST1 45.933 48.636 124.087 90.00 99.27 90.00 P 1 21 1 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 0.021771 0.000000 0.003553 0.00000 SCALE2 0.000000 0.020561 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008166 0.00000 MTRIX1 1 1.000000 0.000000 0.000000 0.00000 1 MTRIX2 1 0.000000 1.000000 0.000000 0.00000 1 MTRIX3 1 0.000000 0.000000 1.000000 0.00000 1