HEADER OXIDOREDUCTASE 31-OCT-14 4D4Z TITLE STRUCTURE OF HUMAN DEOXYHYPUSINE HYDROXYLASE IN COMPLEX WITH GLYCEROL 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: PGEX-6P-1 KEYWDS OXIDOREDUCTASE, EIF-5A, HYPUSINE EXPDTA X-RAY DIFFRACTION AUTHOR Z.HAN,N.SAKAI,R.HILGENFELD REVDAT 3 27-MAY-15 4D4Z 1 JRNL REVDAT 2 22-APR-15 4D4Z 1 JRNL REVDAT 1 15-APR-15 4D4Z 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,VAGIN,DODSON 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) : 19.95 REMARK 3 DATA CUTOFF (SIGMA(F)) : NONE REMARK 3 COMPLETENESS FOR RANGE (%) : 98.14 REMARK 3 NUMBER OF REFLECTIONS : 64571 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) : 0.17140 REMARK 3 R VALUE (WORKING SET) : 0.17024 REMARK 3 FREE R VALUE : 0.19283 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.0 REMARK 3 FREE R VALUE TEST SET COUNT : 3423 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) : 4063 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 84.80 REMARK 3 BIN R VALUE (WORKING SET) : 0.198 REMARK 3 BIN FREE R VALUE SET COUNT : 220 REMARK 3 BIN FREE R VALUE : 0.260 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4459 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 37 REMARK 3 SOLVENT ATOMS : 335 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 17.2 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.665 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.34 REMARK 3 B22 (A**2) : -0.38 REMARK 3 B33 (A**2) : 0.05 REMARK 3 B12 (A**2) : 0.00 REMARK 3 B13 (A**2) : -0.06 REMARK 3 B23 (A**2) : -0.00 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.097 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.092 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.056 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.649 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.962 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.950 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4581 ; 0.021 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 4385 ; 0.006 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6224 ; 2.007 ; 1.984 REMARK 3 BOND ANGLES OTHERS (DEGREES): 10086 ; 1.284 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 594 ; 4.729 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 222 ;37.602 ;23.874 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 745 ;14.843 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 44 ;19.581 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 686 ; 0.129 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5288 ; 0.012 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 1016 ; 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 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED 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 : 1 REMARK 3 REMARK 3 NUMBER OF DIFFERENT NCS PAIRS : 1 REMARK 3 GROUP CHAIN1 RANGE CHAIN2 RANGE COUNT RMS WEIGHT REMARK 3 1 A -5 282 B -5 282 17513 0.09 0.05 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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 REMARK 3 RIDING POSITIONS. REMARK 4 REMARK 4 4D4Z 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-62189. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-JUL-11 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 : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 68054 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.70 REMARK 200 RESOLUTION RANGE LOW (A) : 44.92 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 6.0 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.2 REMARK 200 DATA REDUNDANCY : 4.0 REMARK 200 R MERGE (I) : 0.04 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 23.50 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 (%) : 89.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.0 REMARK 200 R MERGE FOR SHELL (I) : 0.17 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 6.00 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: AUTO-RICKSHAW REMARK 200 STARTING MODEL: NONE REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.49 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30% POLYETHYLENE GLYCOL 6000 REMARK 280 (W/V), 100 MM BIS-TRIS PROPANE PH 7.2 - 7.4, 15% GLYCEROL 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 35.08750 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 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 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 THR A 284 REMARK 465 GLY A 285 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 SER A -1 N MET A 1 2.18 REMARK 500 NE2 GLN A 22 O HOH A 2034 2.17 REMARK 500 O SER B -1 N MET B 1 2.12 REMARK 500 CE2B PHE B 29 O HOH B 2059 1.85 REMARK 500 O HOH B 2008 O HOH B 2009 2.11 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 A 105 CD GLU A 105 OE2 0.085 REMARK 500 ARG A 231 CZ ARG A 231 NH2 0.082 REMARK 500 ARG B 128 CD ARG B 128 NE -0.107 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. = -16.7 DEGREES REMARK 500 ARG A 26 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 ASP A 48 CB - CG - OD1 ANGL. DEV. = 5.7 DEGREES REMARK 500 ASP A 48 CB - CG - OD2 ANGL. DEV. = -6.8 DEGREES REMARK 500 ARG A 162 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 ARG A 162 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 CYS A 200 CB - CA - C ANGL. DEV. = -10.3 DEGREES REMARK 500 GLU A 244 OE1 - CD - OE2 ANGL. DEV. = 7.8 DEGREES REMARK 500 SER B -1 O - C - N ANGL. DEV. = -16.7 DEGREES REMARK 500 MET B 1 C - N - CA ANGL. DEV. = 17.0 DEGREES REMARK 500 MET B 86 CG - SD - CE ANGL. DEV. = -10.5 DEGREES REMARK 500 ARG B 128 CG - CD - NE ANGL. DEV. = -14.5 DEGREES REMARK 500 ARG B 128 NE - CZ - NH1 ANGL. DEV. = 6.6 DEGREES REMARK 500 ARG B 128 NE - CZ - NH2 ANGL. DEV. = -6.1 DEGREES REMARK 500 ARG B 162 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 ARG B 162 NE - CZ - NH2 ANGL. DEV. = -3.3 DEGREES REMARK 500 GLU B 244 OE1 - CD - OE2 ANGL. DEV. = 7.7 DEGREES REMARK 500 ARG B 270 NE - CZ - NH1 ANGL. DEV. = 5.4 DEGREES 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 -11.96 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 172.1 REMARK 620 3 OH A 303 O 93.1 88.2 REMARK 620 4 GOL A 305 O3 87.5 100.4 79.7 REMARK 620 5 HIS A 89 NE2 84.1 88.2 112.4 165.6 REMARK 620 6 GOL A 305 O2 87.8 93.8 158.0 78.4 89.5 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 HIS B 89 NE2 REMARK 620 2 HIS B 207 NE2 89.8 REMARK 620 3 OH B 303 O 114.3 88.1 REMARK 620 4 GOL B 305 O1 163.6 101.2 78.5 REMARK 620 5 GOL B 305 O2 91.0 95.1 154.5 76.1 REMARK 620 6 GLU B 90 OE1 81.2 170.2 92.2 88.5 88.9 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 87.3 REMARK 620 3 OH A 303 O 89.7 112.8 REMARK 620 4 GOL A 305 O3 105.4 166.9 71.1 REMARK 620 5 HOH A2001 O 87.5 87.4 159.4 90.0 REMARK 620 6 GLU A 241 OE1 167.6 81.8 99.9 85.2 86.1 REMARK 620 N 1 2 3 4 5 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 HIS B 240 NE2 REMARK 620 2 HIS B 56 NE2 88.6 REMARK 620 3 HOH B2001 O 87.3 84.7 REMARK 620 4 GLU B 241 OE1 81.0 167.5 87.9 REMARK 620 5 OH B 303 O 118.2 90.8 154.0 100.1 REMARK 620 6 GOL B 305 O1 166.3 104.5 89.7 85.5 66.6 REMARK 620 N 1 2 3 4 5 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 OH A 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 305 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE B3P A 306 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FE B 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FE B 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE OH B 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 305 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4D50 RELATED DB: PDB REMARK 900 STRUCTURE OF HUMAN DEOXYHYPUSINE HYDROXYLASE REMARK 999 REMARK 999 SEQUENCE REMARK 999 FIVE RESIDUES (GPLGS) IN N-TERMINUS ARE FROM EXPRESSION REMARK 999 VECTOR DBREF 4D4Z A 1 289 UNP Q9BU89 DOHH_HUMAN 1 289 DBREF 4D4Z B 1 289 UNP Q9BU89 DOHH_HUMAN 1 289 SEQADV 4D4Z GLY A -5 UNP Q9BU89 EXPRESSION TAG SEQADV 4D4Z PRO A -4 UNP Q9BU89 EXPRESSION TAG SEQADV 4D4Z LEU A -3 UNP Q9BU89 EXPRESSION TAG SEQADV 4D4Z GLY A -2 UNP Q9BU89 EXPRESSION TAG SEQADV 4D4Z SER A -1 UNP Q9BU89 EXPRESSION TAG SEQADV 4D4Z GLY B -5 UNP Q9BU89 EXPRESSION TAG SEQADV 4D4Z PRO B -4 UNP Q9BU89 EXPRESSION TAG SEQADV 4D4Z LEU B -3 UNP Q9BU89 EXPRESSION TAG SEQADV 4D4Z GLY B -2 UNP Q9BU89 EXPRESSION TAG SEQADV 4D4Z 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 OH A 303 1 HET GOL A 305 6 HET B3P A 306 19 HET FE B 301 1 HET FE B 302 1 HET OH B 303 1 HET GOL B 305 6 HETNAM FE FE (III) ION HETNAM OH HYDROXIDE ION HETNAM GOL GLYCEROL HETNAM B3P 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL- HETNAM 2 B3P ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3- HETNAM 3 B3P DIOL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 FE 4(FE 3+) FORMUL 4 OH 2(H O 1-) FORMUL 5 GOL 2(C3 H8 O3) FORMUL 6 B3P C11 H26 N2 O6 FORMUL 7 HOH *335(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 186 GLY A 197 1 12 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 ALA A 262 1 12 HELIX 21 21 GLU A 266 GLU A 283 1 18 HELIX 22 22 LEU B -3 ASP B 16 1 19 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 SER B 111 1 9 HELIX 32 32 VAL B 115 GLY B 136 1 22 HELIX 33 33 ASP B 157 ASP B 167 1 11 HELIX 34 34 PRO B 171 GLY B 186 1 16 HELIX 35 35 GLY B 186 GLY B 197 1 12 HELIX 36 36 LEU B 198 CYS B 200 5 3 HELIX 37 37 SER B 202 GLN B 217 1 16 HELIX 38 38 HIS B 218 ALA B 220 5 3 HELIX 39 39 ALA B 221 ARG B 231 1 11 HELIX 40 40 ASN B 235 ALA B 250 1 16 HELIX 41 41 ARG B 251 HIS B 261 1 11 HELIX 42 42 GLU B 266 THR B 284 1 19 LINK FE FE A 301 OE1 GLU A 90 1555 1555 2.03 LINK FE FE A 301 NE2 HIS A 207 1555 1555 2.18 LINK FE FE A 301 O OH A 303 1555 1555 2.05 LINK FE FE A 301 O3 GOL A 305 1555 1555 2.08 LINK FE FE A 301 NE2 HIS A 89 1555 1555 2.22 LINK FE FE A 301 O2 GOL A 305 1555 1555 2.18 LINK FE FE A 302 NE2 HIS A 56 1555 1555 2.24 LINK FE FE A 302 OE1 GLU A 241 1555 1555 2.00 LINK FE FE A 302 O HOH A2001 1555 1555 2.09 LINK FE FE A 302 O3 GOL A 305 1555 1555 2.34 LINK FE FE A 302 O OH A 303 1555 1555 2.21 LINK FE FE A 302 NE2 HIS A 240 1555 1555 2.29 LINK FE FE B 301 OE1 GLU B 90 1555 1555 2.10 LINK FE FE B 301 O2 GOL B 305 1555 1555 2.19 LINK FE FE B 301 O1 GOL B 305 1555 1555 2.07 LINK FE FE B 301 O OH B 303 1555 1555 1.95 LINK FE FE B 301 NE2 HIS B 207 1555 1555 2.18 LINK FE FE B 301 NE2 HIS B 89 1555 1555 2.22 LINK FE FE B 302 NE2 HIS B 56 1555 1555 2.26 LINK FE FE B 302 O HOH B2001 1555 1555 2.02 LINK FE FE B 302 OE1 GLU B 241 1555 1555 1.99 LINK FE FE B 302 O OH B 303 1555 1555 2.22 LINK FE FE B 302 O1 GOL B 305 1555 1555 2.41 LINK FE FE B 302 NE2 HIS B 240 1555 1555 2.29 SITE 1 AC1 6 HIS A 89 GLU A 90 HIS A 207 FE A 302 SITE 2 AC1 6 OH A 303 GOL A 305 SITE 1 AC2 7 HIS A 56 HIS A 240 GLU A 241 FE A 301 SITE 2 AC2 7 OH A 303 GOL A 305 HOH A2001 SITE 1 AC3 9 HIS A 56 HIS A 89 GLU A 90 HIS A 207 SITE 2 AC3 9 MET A 237 GLU A 241 FE A 301 FE A 302 SITE 3 AC3 9 GOL A 305 SITE 1 AC4 10 HIS A 56 HIS A 89 GLU A 90 GLU A 93 SITE 2 AC4 10 HIS A 207 GLU A 208 GLU A 241 FE A 301 SITE 3 AC4 10 FE A 302 OH A 303 SITE 1 AC5 6 PHE A 47 ASP A 48 ASP A 76 ASP A 80 SITE 2 AC5 6 GLN A 83 HOH A2058 SITE 1 AC6 6 HIS B 89 GLU B 90 HIS B 207 FE B 302 SITE 2 AC6 6 OH B 303 GOL B 305 SITE 1 AC7 7 HIS B 56 HIS B 240 GLU B 241 FE B 301 SITE 2 AC7 7 OH B 303 GOL B 305 HOH B2001 SITE 1 AC8 8 HIS B 56 HIS B 89 GLU B 90 HIS B 207 SITE 2 AC8 8 GLU B 241 FE B 301 FE B 302 GOL B 305 SITE 1 AC9 10 HIS B 56 HIS B 89 GLU B 90 GLU B 93 SITE 2 AC9 10 HIS B 207 GLU B 208 GLU B 241 FE B 301 SITE 3 AC9 10 FE B 302 OH B 303 CRYST1 46.051 70.175 101.275 90.00 102.71 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 0.021715 0.000000 0.004898 0.00000 SCALE2 0.000000 0.014250 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010122 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