HEADER OXIDOREDUCTASE 11-FEB-15 4Y4R TITLE CRYSTAL STRUCTURE OF RIBOSOMAL OXYGENASE NO66 DIMER MUTANT COMPND MOL_ID: 1; COMPND 2 MOLECULE: BIFUNCTIONAL LYSINE-SPECIFIC DEMETHYLASE AND HISTIDYL- COMPND 3 HYDROXYLASE NO66; COMPND 4 CHAIN: A, B; COMPND 5 FRAGMENT: UNP RESIDUES 176-525, 541-641; COMPND 6 SYNONYM: 60S RIBOSOMAL PROTEIN L8 HISTIDINE HYDROXYLASE,HISTONE COMPND 7 LYSINE DEMETHYLASE NO66,MYC-ASSOCIATED PROTEIN WITH JMJC DOMAIN, COMPND 8 NUCLEOLAR PROTEIN 66,HSNO66,RIBOSOMAL OXYGENASE NO66,ROX; COMPND 9 EC: 1.14.11.-,1.14.11.27; COMPND 10 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: NO66, C14ORF169, MAPJD; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET28A KEYWDS RIBOSOMAL OXYGENASE, NO66, DIMER MUTANT, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR C.WANG,T.HANG,J.ZANG REVDAT 2 20-MAR-24 4Y4R 1 REMARK LINK REVDAT 1 07-OCT-15 4Y4R 0 JRNL AUTH C.WANG,Q.ZHANG,T.HANG,Y.TAO,X.MA,M.WU,X.ZHANG,J.ZANG JRNL TITL STRUCTURE OF THE JMJC DOMAIN-CONTAINING PROTEIN NO66 JRNL TITL 2 COMPLEXED WITH RIBOSOMAL PROTEIN RPL8. JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 71 1955 2015 JRNL REFN ESSN 1399-0047 JRNL PMID 26327385 JRNL DOI 10.1107/S1399004715012948 REMARK 2 REMARK 2 RESOLUTION. 3.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.7.0032 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) : 3.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 3 NUMBER OF REFLECTIONS : 25870 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) : 0.220 REMARK 3 R VALUE (WORKING SET) : 0.217 REMARK 3 FREE R VALUE : 0.271 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1372 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) : 3.30 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.39 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1811 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.31 REMARK 3 BIN R VALUE (WORKING SET) : 0.2920 REMARK 3 BIN FREE R VALUE SET COUNT : 104 REMARK 3 BIN FREE R VALUE : 0.3260 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 7072 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 6 REMARK 3 SOLVENT ATOMS : 4 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 99.44 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.98000 REMARK 3 B22 (A**2) : -1.08000 REMARK 3 B33 (A**2) : 2.06000 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): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.478 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.373 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 23.085 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.925 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.884 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 7258 ; 0.014 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 6758 ; 0.005 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 9875 ; 1.620 ; 1.964 REMARK 3 BOND ANGLES OTHERS (DEGREES): 15474 ; 0.848 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 885 ; 6.878 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 363 ;33.867 ;22.865 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1140 ;19.540 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 72 ;23.304 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 1066 ; 0.080 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 8303 ; 0.006 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 1769 ; 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): 3553 ; 6.946 ; 9.890 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 3551 ; 6.948 ; 9.889 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4433 ;10.475 ;14.829 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 4434 ;10.474 ;14.831 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 3705 ; 7.117 ;10.219 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 3706 ; 7.116 ;10.217 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 5443 ;10.919 ;15.183 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 8199 ;13.871 ;78.008 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 8193 ;13.871 ;78.030 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 REMARK 4 REMARK 4 4Y4R COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 27-FEB-15. REMARK 100 THE DEPOSITION ID IS D_1000206827. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-SEP-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL17U REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9791 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 27284 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.300 REMARK 200 RESOLUTION RANGE LOW (A) : 64.580 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 200 DATA REDUNDANCY : 6.200 REMARK 200 R MERGE (I) : 0.10100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.48 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.0 REMARK 200 DATA REDUNDANCY IN SHELL : 5.60 REMARK 200 R MERGE FOR SHELL (I) : 0.61300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 71.65 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.34 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.0M AMMONIUM MONOHYDRIC PHOSPHATE, REMARK 280 0.1M ACETATE PH4.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 289K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 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 43.03000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 72.10500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 72.10500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 72.10500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 43.03000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 72.10500 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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: 7100 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 37240 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -66.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 GLY A 176 REMARK 465 GLY A 177 REMARK 465 GLU A 178 REMARK 465 PRO A 179 REMARK 465 ALA A 180 REMARK 465 LEU A 628 REMARK 465 ASN A 629 REMARK 465 GLY B 176 REMARK 465 GLY B 177 REMARK 465 GLU B 178 REMARK 465 GLY B 526 REMARK 465 GLY B 527 REMARK 465 GLY B 528 REMARK 465 THR B 534 REMARK 465 GLU B 535 REMARK 465 VAL B 536 REMARK 465 ALA B 627 REMARK 465 LEU B 628 REMARK 465 ASN B 629 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 TRP A 181 CG CD1 CD2 NE1 CE2 CE3 CZ2 REMARK 470 TRP A 181 CZ3 CH2 REMARK 470 ASN A 269 CG OD1 ND2 REMARK 470 ARG A 272 CG CD NE CZ NH1 NH2 REMARK 470 VAL A 364 CG1 CG2 REMARK 470 GLN A 379 CG CD OE1 NE2 REMARK 470 LYS A 470 CG CD CE NZ REMARK 470 GLU A 568 CG CD OE1 OE2 REMARK 470 GLU A 569 CG CD OE1 OE2 REMARK 470 GLU A 605 CG CD OE1 OE2 REMARK 470 ARG B 187 CG CD NE CZ NH1 NH2 REMARK 470 ASN B 269 CG OD1 ND2 REMARK 470 LEU B 296 CG CD1 CD2 REMARK 470 VAL B 364 CG1 CG2 REMARK 470 LYS B 470 CG CD CE NZ REMARK 470 GLN B 529 CG CD OE1 NE2 REMARK 470 LEU B 530 CG CD1 CD2 REMARK 470 GLU B 568 CG CD OE1 OE2 REMARK 470 GLU B 569 CG CD OE1 OE2 REMARK 470 THR B 612 OG1 CG2 REMARK 470 LEU B 626 CG CD1 CD2 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 OG SER A 295 OG1 THR A 330 2.05 REMARK 500 O ASN B 269 NH1 ARG B 271 2.16 REMARK 500 OD2 ASP A 234 OG1 THR A 236 2.18 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 479 CG GLU A 479 CD 0.203 REMARK 500 GLU A 479 CD GLU A 479 OE1 0.210 REMARK 500 GLU A 479 CD GLU A 479 OE2 0.163 REMARK 500 GLY A 527 N GLY A 527 CA 0.110 REMARK 500 GLN A 579 CD GLN A 579 OE1 0.179 REMARK 500 PRO B 179 N PRO B 179 CA 0.136 REMARK 500 GLU B 479 CG GLU B 479 CD 0.112 REMARK 500 GLU B 479 CD GLU B 479 OE1 0.113 REMARK 500 GLU B 479 CD GLU B 479 OE2 0.094 REMARK 500 GLN B 579 CD GLN B 579 OE1 0.185 REMARK 500 GLU B 605 CG GLU B 605 CD 0.107 REMARK 500 GLU B 605 CD GLU B 605 OE1 0.123 REMARK 500 GLU B 605 CD GLU B 605 OE2 0.098 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 ASP A 499 CB - CG - OD1 ANGL. DEV. = 5.7 DEGREES REMARK 500 PRO B 332 C - N - CA ANGL. DEV. = 9.1 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 GLU A 224 -5.83 71.63 REMARK 500 PRO A 278 152.07 -44.27 REMARK 500 ALA A 281 107.72 -57.70 REMARK 500 ARG A 361 139.95 -39.71 REMARK 500 PHE A 399 140.44 -170.64 REMARK 500 GLN A 410 -159.87 -134.71 REMARK 500 ASP A 411 -135.62 49.82 REMARK 500 LEU A 454 178.96 -59.84 REMARK 500 SER A 469 153.75 -41.77 REMARK 500 HIS A 490 2.34 -62.19 REMARK 500 VAL A 523 5.21 -66.83 REMARK 500 HIS A 566 2.65 58.99 REMARK 500 ALA A 580 -36.46 -34.83 REMARK 500 ALA A 582 -70.48 -65.96 REMARK 500 PRO A 591 49.15 -105.61 REMARK 500 PRO A 600 108.19 -56.14 REMARK 500 ASP B 182 -41.73 -133.28 REMARK 500 GLU B 224 -7.34 65.10 REMARK 500 CYS B 300 77.66 51.05 REMARK 500 MET B 322 134.76 -35.13 REMARK 500 ALA B 370 157.19 -48.92 REMARK 500 GLN B 410 -154.15 -130.97 REMARK 500 ASP B 411 -125.84 49.27 REMARK 500 TYR B 423 34.56 71.51 REMARK 500 ALA B 496 -34.49 -37.28 REMARK 500 THR B 532 -7.31 -53.95 REMARK 500 HIS B 552 -169.52 -104.89 REMARK 500 VAL B 559 1.84 -62.96 REMARK 500 HIS B 566 18.11 51.54 REMARK 500 PRO B 591 59.25 -96.69 REMARK 500 PRO B 600 69.66 -63.47 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 NI A 701 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 340 NE2 REMARK 620 2 HIS A 405 NE2 76.7 REMARK 620 3 ACT A 702 OXT 123.7 120.4 REMARK 620 4 HOH A 801 O 59.1 122.5 68.4 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NI B 701 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 340 NE2 REMARK 620 2 ASP B 342 OD2 120.6 REMARK 620 3 HIS B 405 NE2 89.4 101.0 REMARK 620 4 HOH B 802 O 100.3 79.5 168.4 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NI A 701 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACT A 702 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NI B 701 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4Y33 RELATED DB: PDB REMARK 900 RELATED ID: 4Y3O RELATED DB: PDB DBREF 4Y4R A 176 525 UNP Q9H6W3 NO66_HUMAN 176 525 DBREF 4Y4R A 529 629 UNP Q9H6W3 NO66_HUMAN 541 641 DBREF 4Y4R B 176 525 UNP Q9H6W3 NO66_HUMAN 176 525 DBREF 4Y4R B 529 629 UNP Q9H6W3 NO66_HUMAN 541 641 SEQADV 4Y4R GLY A 526 UNP Q9H6W3 LINKER SEQADV 4Y4R GLY A 527 UNP Q9H6W3 LINKER SEQADV 4Y4R GLY A 528 UNP Q9H6W3 LINKER SEQADV 4Y4R GLY B 526 UNP Q9H6W3 LINKER SEQADV 4Y4R GLY B 527 UNP Q9H6W3 LINKER SEQADV 4Y4R GLY B 528 UNP Q9H6W3 LINKER SEQRES 1 A 454 GLY GLY GLU PRO ALA TRP ASP SER PRO LEU ARG ARG VAL SEQRES 2 A 454 LEU ALA GLU LEU ASN ARG ILE PRO SER SER ARG ARG ARG SEQRES 3 A 454 ALA ALA ARG LEU PHE GLU TRP LEU ILE ALA PRO MET PRO SEQRES 4 A 454 PRO ASP HIS PHE TYR ARG ARG LEU TRP GLU ARG GLU ALA SEQRES 5 A 454 VAL LEU VAL ARG ARG GLN ASP HIS THR TYR TYR GLN GLY SEQRES 6 A 454 LEU PHE SER THR ALA ASP LEU ASP SER MET LEU ARG ASN SEQRES 7 A 454 GLU GLU VAL GLN PHE GLY GLN HIS LEU ASP ALA ALA ARG SEQRES 8 A 454 TYR ILE ASN GLY ARG ARG GLU THR LEU ASN PRO PRO GLY SEQRES 9 A 454 ARG ALA LEU PRO ALA ALA ALA TRP SER LEU TYR GLN ALA SEQRES 10 A 454 GLY CYS SER LEU ARG LEU LEU CYS PRO GLN ALA PHE SER SEQRES 11 A 454 THR THR VAL TRP GLN PHE LEU ALA VAL LEU GLN GLU GLN SEQRES 12 A 454 PHE GLY SER MET ALA GLY SER ASN VAL TYR LEU THR PRO SEQRES 13 A 454 PRO ASN SER GLN GLY PHE ALA PRO HIS TYR ASP ASP ILE SEQRES 14 A 454 GLU ALA PHE VAL LEU GLN LEU GLU GLY ARG LYS LEU TRP SEQRES 15 A 454 ARG VAL TYR ARG PRO ARG VAL PRO THR GLU GLU LEU ALA SEQRES 16 A 454 LEU THR SER SER PRO ASN PHE SER GLN ASP ASP LEU GLY SEQRES 17 A 454 GLU PRO VAL LEU GLN THR VAL LEU GLU PRO GLY ASP LEU SEQRES 18 A 454 LEU TYR PHE PRO ARG GLY PHE ILE HIS GLN ALA GLU CYS SEQRES 19 A 454 GLN ASP GLY VAL HIS SER LEU HIS LEU THR LEU SER THR SEQRES 20 A 454 TYR GLN ARG ASN THR TRP GLY ASP PHE LEU GLU ALA ILE SEQRES 21 A 454 LEU PRO LEU ALA VAL GLN ALA ALA MET GLU GLU ASN VAL SEQRES 22 A 454 GLU PHE ARG ARG GLY LEU PRO ARG ASP PHE MET ASP TYR SEQRES 23 A 454 MET GLY ALA GLN HIS SER ASP SER LYS ASP PRO ARG ARG SEQRES 24 A 454 THR ALA PHE MET GLU LYS VAL ARG VAL LEU VAL ALA ARG SEQRES 25 A 454 LEU GLY HIS PHE ALA PRO VAL ASP ALA VAL ALA ASP GLN SEQRES 26 A 454 ARG ALA LYS ASP PHE ILE HIS ASP SER LEU PRO PRO VAL SEQRES 27 A 454 LEU THR ASP ARG GLU ARG ALA LEU SER VAL TYR GLY GLY SEQRES 28 A 454 GLY GLY GLN LEU THR THR GLU THR GLU VAL HIS MET LEU SEQRES 29 A 454 GLN ASP GLY ILE ALA ARG LEU VAL GLY GLU GLY GLY HIS SEQRES 30 A 454 LEU PHE LEU TYR TYR THR VAL GLU ASN SER ARG VAL TYR SEQRES 31 A 454 HIS LEU GLU GLU PRO LYS CYS LEU GLU ILE TYR PRO GLN SEQRES 32 A 454 GLN ALA ASP ALA MET GLU LEU LEU LEU GLY SER TYR PRO SEQRES 33 A 454 GLU PHE VAL ARG VAL GLY ASP LEU PRO CYS ASP SER VAL SEQRES 34 A 454 GLU ASP GLN LEU SER LEU ALA THR THR LEU TYR ASP LYS SEQRES 35 A 454 GLY LEU LEU LEU THR LYS MET PRO LEU ALA LEU ASN SEQRES 1 B 454 GLY GLY GLU PRO ALA TRP ASP SER PRO LEU ARG ARG VAL SEQRES 2 B 454 LEU ALA GLU LEU ASN ARG ILE PRO SER SER ARG ARG ARG SEQRES 3 B 454 ALA ALA ARG LEU PHE GLU TRP LEU ILE ALA PRO MET PRO SEQRES 4 B 454 PRO ASP HIS PHE TYR ARG ARG LEU TRP GLU ARG GLU ALA SEQRES 5 B 454 VAL LEU VAL ARG ARG GLN ASP HIS THR TYR TYR GLN GLY SEQRES 6 B 454 LEU PHE SER THR ALA ASP LEU ASP SER MET LEU ARG ASN SEQRES 7 B 454 GLU GLU VAL GLN PHE GLY GLN HIS LEU ASP ALA ALA ARG SEQRES 8 B 454 TYR ILE ASN GLY ARG ARG GLU THR LEU ASN PRO PRO GLY SEQRES 9 B 454 ARG ALA LEU PRO ALA ALA ALA TRP SER LEU TYR GLN ALA SEQRES 10 B 454 GLY CYS SER LEU ARG LEU LEU CYS PRO GLN ALA PHE SER SEQRES 11 B 454 THR THR VAL TRP GLN PHE LEU ALA VAL LEU GLN GLU GLN SEQRES 12 B 454 PHE GLY SER MET ALA GLY SER ASN VAL TYR LEU THR PRO SEQRES 13 B 454 PRO ASN SER GLN GLY PHE ALA PRO HIS TYR ASP ASP ILE SEQRES 14 B 454 GLU ALA PHE VAL LEU GLN LEU GLU GLY ARG LYS LEU TRP SEQRES 15 B 454 ARG VAL TYR ARG PRO ARG VAL PRO THR GLU GLU LEU ALA SEQRES 16 B 454 LEU THR SER SER PRO ASN PHE SER GLN ASP ASP LEU GLY SEQRES 17 B 454 GLU PRO VAL LEU GLN THR VAL LEU GLU PRO GLY ASP LEU SEQRES 18 B 454 LEU TYR PHE PRO ARG GLY PHE ILE HIS GLN ALA GLU CYS SEQRES 19 B 454 GLN ASP GLY VAL HIS SER LEU HIS LEU THR LEU SER THR SEQRES 20 B 454 TYR GLN ARG ASN THR TRP GLY ASP PHE LEU GLU ALA ILE SEQRES 21 B 454 LEU PRO LEU ALA VAL GLN ALA ALA MET GLU GLU ASN VAL SEQRES 22 B 454 GLU PHE ARG ARG GLY LEU PRO ARG ASP PHE MET ASP TYR SEQRES 23 B 454 MET GLY ALA GLN HIS SER ASP SER LYS ASP PRO ARG ARG SEQRES 24 B 454 THR ALA PHE MET GLU LYS VAL ARG VAL LEU VAL ALA ARG SEQRES 25 B 454 LEU GLY HIS PHE ALA PRO VAL ASP ALA VAL ALA ASP GLN SEQRES 26 B 454 ARG ALA LYS ASP PHE ILE HIS ASP SER LEU PRO PRO VAL SEQRES 27 B 454 LEU THR ASP ARG GLU ARG ALA LEU SER VAL TYR GLY GLY SEQRES 28 B 454 GLY GLY GLN LEU THR THR GLU THR GLU VAL HIS MET LEU SEQRES 29 B 454 GLN ASP GLY ILE ALA ARG LEU VAL GLY GLU GLY GLY HIS SEQRES 30 B 454 LEU PHE LEU TYR TYR THR VAL GLU ASN SER ARG VAL TYR SEQRES 31 B 454 HIS LEU GLU GLU PRO LYS CYS LEU GLU ILE TYR PRO GLN SEQRES 32 B 454 GLN ALA ASP ALA MET GLU LEU LEU LEU GLY SER TYR PRO SEQRES 33 B 454 GLU PHE VAL ARG VAL GLY ASP LEU PRO CYS ASP SER VAL SEQRES 34 B 454 GLU ASP GLN LEU SER LEU ALA THR THR LEU TYR ASP LYS SEQRES 35 B 454 GLY LEU LEU LEU THR LYS MET PRO LEU ALA LEU ASN HET NI A 701 1 HET ACT A 702 4 HET NI B 701 1 HETNAM NI NICKEL (II) ION HETNAM ACT ACETATE ION FORMUL 3 NI 2(NI 2+) FORMUL 4 ACT C2 H3 O2 1- FORMUL 6 HOH *4(H2 O) HELIX 1 AA1 SER A 183 ASN A 193 1 11 HELIX 2 AA2 SER A 197 ALA A 211 1 15 HELIX 3 AA3 PRO A 214 LEU A 222 1 9 HELIX 4 AA4 SER A 243 GLU A 254 1 12 HELIX 5 AA5 LEU A 282 ALA A 292 1 11 HELIX 6 AA6 CYS A 300 SER A 305 1 6 HELIX 7 AA7 SER A 305 GLY A 320 1 16 HELIX 8 AA8 VAL A 364 GLU A 368 5 5 HELIX 9 AA9 SER A 378 LEU A 382 5 5 HELIX 10 AB1 THR A 427 ASN A 447 1 21 HELIX 11 AB2 VAL A 448 ARG A 451 5 4 HELIX 12 AB3 ASP A 457 TYR A 461 5 5 HELIX 13 AB4 ALA A 464 ASP A 468 5 5 HELIX 14 AB5 ARG A 473 HIS A 490 1 18 HELIX 15 AB6 PRO A 493 SER A 509 1 17 HELIX 16 AB7 THR A 515 SER A 522 1 8 HELIX 17 AB8 GLN A 579 SER A 589 1 11 HELIX 18 AB9 GLY A 597 LEU A 599 5 3 HELIX 19 AC1 SER A 603 LYS A 617 1 15 HELIX 20 AC2 SER B 183 ARG B 194 1 12 HELIX 21 AC3 SER B 197 ALA B 211 1 15 HELIX 22 AC4 PRO B 214 LEU B 222 1 9 HELIX 23 AC5 SER B 243 GLU B 254 1 12 HELIX 24 AC6 LEU B 282 ALA B 292 1 11 HELIX 25 AC7 SER B 305 GLY B 320 1 16 HELIX 26 AC8 VAL B 364 GLU B 368 5 5 HELIX 27 AC9 THR B 427 ASN B 447 1 21 HELIX 28 AD1 VAL B 448 ARG B 452 5 5 HELIX 29 AD2 ASP B 457 TYR B 461 5 5 HELIX 30 AD3 GLY B 463 SER B 467 5 5 HELIX 31 AD4 ARG B 473 ALA B 492 1 20 HELIX 32 AD5 PRO B 493 SER B 509 1 17 HELIX 33 AD6 THR B 515 SER B 522 1 8 HELIX 34 AD7 TYR B 576 SER B 589 1 14 HELIX 35 AD8 ARG B 595 LEU B 599 5 5 HELIX 36 AD9 SER B 603 LYS B 617 1 15 SHEET 1 AA1 8 VAL A 228 VAL A 230 0 SHEET 2 AA1 8 LEU A 396 PHE A 399 -1 O LEU A 396 N VAL A 230 SHEET 3 AA1 8 GLU A 345 GLY A 353 -1 N VAL A 348 O LEU A 397 SHEET 4 AA1 8 SER A 415 THR A 422 -1 O LEU A 418 N LEU A 349 SHEET 5 AA1 8 GLY A 324 THR A 330 -1 N TYR A 328 O HIS A 417 SHEET 6 AA1 8 SER A 295 LEU A 298 -1 N LEU A 298 O VAL A 327 SHEET 7 AA1 8 LEU A 262 ILE A 268 -1 N ALA A 265 O SER A 295 SHEET 8 AA1 8 ARG A 271 THR A 274 -1 O ARG A 271 N ILE A 268 SHEET 1 AA2 4 HIS A 340 TYR A 341 0 SHEET 2 AA2 4 ILE A 404 GLU A 408 -1 O HIS A 405 N HIS A 340 SHEET 3 AA2 4 LYS A 355 TYR A 360 -1 N TYR A 360 O ILE A 404 SHEET 4 AA2 4 LEU A 387 LEU A 391 -1 O THR A 389 N TRP A 357 SHEET 1 AA3 3 VAL A 594 ARG A 595 0 SHEET 2 AA3 3 GLU A 535 MET A 538 -1 N VAL A 536 O VAL A 594 SHEET 3 AA3 3 LEU A 620 THR A 622 -1 O LEU A 621 N HIS A 537 SHEET 1 AA4 3 ALA A 544 GLY A 548 0 SHEET 2 AA4 3 LEU A 553 TYR A 557 -1 O PHE A 554 N VAL A 547 SHEET 3 AA4 3 CYS A 572 GLU A 574 -1 O LEU A 573 N LEU A 555 SHEET 1 AA5 8 VAL B 228 VAL B 230 0 SHEET 2 AA5 8 LEU B 396 PHE B 399 -1 O LEU B 396 N VAL B 230 SHEET 3 AA5 8 GLU B 345 GLY B 353 -1 N VAL B 348 O LEU B 397 SHEET 4 AA5 8 SER B 415 THR B 422 -1 O LEU B 416 N LEU B 351 SHEET 5 AA5 8 GLY B 324 THR B 330 -1 N TYR B 328 O HIS B 417 SHEET 6 AA5 8 SER B 295 LEU B 299 -1 N LEU B 298 O VAL B 327 SHEET 7 AA5 8 ASP B 263 ILE B 268 -1 N ALA B 265 O SER B 295 SHEET 8 AA5 8 ARG B 271 THR B 274 -1 O GLU B 273 N ARG B 266 SHEET 1 AA6 3 LEU B 387 LEU B 391 0 SHEET 2 AA6 3 LYS B 355 VAL B 359 -1 N VAL B 359 O LEU B 387 SHEET 3 AA6 3 HIS B 405 GLU B 408 -1 O GLU B 408 N LEU B 356 SHEET 1 AA7 3 ALA B 544 VAL B 547 0 SHEET 2 AA7 3 PHE B 554 TYR B 557 -1 O PHE B 554 N VAL B 547 SHEET 3 AA7 3 CYS B 572 GLU B 574 -1 O LEU B 573 N LEU B 555 LINK NE2 HIS A 340 NI NI A 701 1555 1555 2.22 LINK NE2 HIS A 405 NI NI A 701 1555 1555 2.29 LINK NI NI A 701 OXT ACT A 702 1555 1555 2.57 LINK NI NI A 701 O HOH A 801 1555 1555 2.57 LINK NE2 HIS B 340 NI NI B 701 1555 1555 2.41 LINK OD2 ASP B 342 NI NI B 701 1555 1555 2.60 LINK NE2 HIS B 405 NI NI B 701 1555 1555 2.23 LINK NI NI B 701 O HOH B 802 1555 1555 2.04 CISPEP 1 ALA A 211 PRO A 212 0 12.46 CISPEP 2 TYR A 590 PRO A 591 0 -3.77 CISPEP 3 ALA B 211 PRO B 212 0 9.56 CISPEP 4 TYR B 590 PRO B 591 0 -5.80 SITE 1 AC1 5 HIS A 340 ASP A 342 HIS A 405 ACT A 702 SITE 2 AC1 5 HOH A 801 SITE 1 AC2 5 TYR A 328 HIS A 340 HIS A 417 NI A 701 SITE 2 AC2 5 HOH A 801 SITE 1 AC3 6 HIS B 340 ASP B 342 HIS B 405 HOH B 801 SITE 2 AC3 6 HOH B 802 HOH B 803 CRYST1 86.060 144.210 144.210 90.00 90.00 90.00 P 21 21 21 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 0.011620 0.000000 0.000000 0.00000 SCALE2 0.000000 0.006934 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006934 0.00000