HEADER OXIDOREDUCTASE 11-JAN-05 1YI9 TITLE CRYSTAL STRUCTURE ANALYSIS OF THE OXIDIZED FORM OF THE M314I MUTANT OF TITLE 2 PEPTIDYLGLYCINE ALPHA-HYDROXYLATING MONOOXYGENASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: PEPTIDYL-GLYCINE ALPHA-AMIDATING MONOOXYGENASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: PEPTIDYLGLYCINE ALPHA-HYDROXYLATING MONOOXYGENASE (RESIDUES COMPND 5 47-355); COMPND 6 SYNONYM: PAM; COMPND 7 EC: 1.14.17.3; COMPND 8 ENGINEERED: YES; COMPND 9 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RATTUS NORVEGICUS; SOURCE 3 ORGANISM_COMMON: NORWAY RAT; SOURCE 4 ORGANISM_TAXID: 10116; SOURCE 5 GENE: PAM; SOURCE 6 EXPRESSION_SYSTEM: CRICETULUS GRISEUS; SOURCE 7 EXPRESSION_SYSTEM_COMMON: CHINESE HAMSTER; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 10029; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: DG44; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: VIRUS; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PCIS KEYWDS MONOOXYGENASE, BIOACTIVE PEPTIDE ACTIVATION, ASCORBATE, KEYWDS 2 OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR X.SIEBERT,B.A.EIPPER,R.E.MAINS,S.T.PRIGGE,N.J.BLACKBURN,L.M.AMZEL REVDAT 4 20-OCT-21 1YI9 1 REMARK SEQADV LINK REVDAT 3 13-JUL-11 1YI9 1 VERSN REVDAT 2 24-FEB-09 1YI9 1 VERSN REVDAT 1 15-NOV-05 1YI9 0 JRNL AUTH X.SIEBERT,B.A.EIPPER,R.E.MAINS,S.T.PRIGGE,N.J.BLACKBURN, JRNL AUTH 2 L.M.AMZEL JRNL TITL THE CATALYTIC COPPER OF PEPTIDYLGLYCINE ALPHA-HYDROXYLATING JRNL TITL 2 MONOOXYGENASE ALSO PLAYS A CRITICAL STRUCTURAL ROLE. JRNL REF BIOPHYS.J. V. 89 3312 2005 JRNL REFN ISSN 0006-3495 JRNL PMID 16100265 JRNL DOI 10.1529/BIOPHYSJ.105.066100 REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0003 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.20 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 87.0 REMARK 3 NUMBER OF REFLECTIONS : 25769 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) : 0.202 REMARK 3 R VALUE (WORKING SET) : 0.201 REMARK 3 FREE R VALUE : 0.233 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1377 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) : 1.70 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.74 REMARK 3 REFLECTION IN BIN (WORKING SET) : 890 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 41.50 REMARK 3 BIN R VALUE (WORKING SET) : 0.2780 REMARK 3 BIN FREE R VALUE SET COUNT : 50 REMARK 3 BIN FREE R VALUE : 0.3390 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2313 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 16 REMARK 3 SOLVENT ATOMS : 132 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 41.70 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 41.69 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.76000 REMARK 3 B22 (A**2) : 0.21000 REMARK 3 B33 (A**2) : -0.96000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.143 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.130 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.101 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 6.359 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.960 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.944 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2402 ; 0.025 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 2137 ; 0.005 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3259 ; 2.182 ; 1.941 REMARK 3 BOND ANGLES OTHERS (DEGREES): 4971 ; 1.058 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 293 ; 8.539 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 102 ;35.821 ;23.039 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 373 ;16.302 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 14 ;21.699 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 352 ; 0.148 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2643 ; 0.010 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 496 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 482 ; 0.235 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 2165 ; 0.214 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1144 ; 0.195 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 1521 ; 0.099 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 141 ; 0.201 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): 1 ; 0.149 ; 0.200 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): 19 ; 0.383 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 70 ; 0.265 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 13 ; 0.200 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 1833 ; 2.023 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 590 ; 0.432 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2402 ; 2.352 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1086 ; 3.540 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 857 ; 4.640 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 47 A 200 REMARK 3 RESIDUE RANGE : A 201 A 355 REMARK 3 ORIGIN FOR THE GROUP (A): 29.9607 25.8268 49.9494 REMARK 3 T TENSOR REMARK 3 T11: -0.1511 T22: -0.1690 REMARK 3 T33: -0.1106 T12: -0.0085 REMARK 3 T13: 0.0368 T23: 0.0122 REMARK 3 L TENSOR REMARK 3 L11: 1.4408 L22: 1.2311 REMARK 3 L33: 3.4478 L12: 0.5043 REMARK 3 L13: 0.7632 L23: 1.0230 REMARK 3 S TENSOR REMARK 3 S11: 0.0477 S12: -0.1796 S13: 0.0761 REMARK 3 S21: 0.2003 S22: -0.1092 S23: 0.1871 REMARK 3 S31: 0.1039 S32: -0.3446 S33: 0.0615 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 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 1YI9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 18-JAN-05. REMARK 100 THE DEPOSITION ID IS D_1000031542. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-APR-03 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X25 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.1 REMARK 200 MONOCHROMATOR : DOUBLE SI CRYSTAL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : CCP4 (SCALA) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 28704 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 48.200 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 87.6 REMARK 200 DATA REDUNDANCY : 2.500 REMARK 200 R MERGE (I) : 0.04100 REMARK 200 R SYM (I) : 0.04100 REMARK 200 FOR THE DATA SET : 8.8000 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 (%) : 48.8 REMARK 200 DATA REDUNDANCY IN SHELL : 1.40 REMARK 200 R MERGE FOR SHELL (I) : 0.37500 REMARK 200 R SYM FOR SHELL (I) : 0.37500 REMARK 200 FOR SHELL : 1.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: PDB ENTRY 1OPM REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 37.30 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.00 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 4000, MAGNESIUM CHLORIDE, TRIS , REMARK 280 PH 8.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K 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 29.73950 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 35.02450 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 33.22900 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 35.02450 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 29.73950 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 33.22900 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: 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 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 299 REMARK 465 ARG A 300 REMARK 465 THR A 301 REMARK 465 GLU A 302 REMARK 465 ALA A 303 REMARK 465 THR A 304 REMARK 465 HIS A 305 REMARK 465 ILE A 306 REMARK 465 GLY A 307 REMARK 465 GLY A 308 REMARK 465 THR A 309 REMARK 465 SER A 310 REMARK 465 SER A 311 REMARK 465 ASP A 312 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 ASP A 104 NH2 ARG A 143 2.05 REMARK 500 OD1 ASP A 58 O HOH A 759 2.11 REMARK 500 NE2 HIS A 244 O HOH A 842 2.12 REMARK 500 N LYS A 230 O1 GOL A 703 2.13 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 177 CB SER A 177 OG 0.269 REMARK 500 ARG A 254 CD ARG A 254 NE -0.108 REMARK 500 GLU A 324 CD GLU A 324 OE2 -0.073 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG A 85 NE - CZ - NH2 ANGL. DEV. = 5.1 DEGREES REMARK 500 LYS A 165 CD - CE - NZ ANGL. DEV. = -15.9 DEGREES REMARK 500 ASP A 211 CB - CG - OD2 ANGL. DEV. = 6.3 DEGREES REMARK 500 ASP A 224 CB - CG - OD2 ANGL. DEV. = 6.5 DEGREES REMARK 500 ARG A 254 NE - CZ - NH1 ANGL. DEV. = 7.3 DEGREES REMARK 500 ARG A 254 NE - CZ - NH2 ANGL. DEV. = -7.1 DEGREES REMARK 500 ARG A 256 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 ASP A 58 -159.98 -150.36 REMARK 500 ASP A 77 32.43 74.03 REMARK 500 SER A 102 86.05 -49.55 REMARK 500 MET A 103 24.99 -66.49 REMARK 500 ASP A 104 -76.82 -97.75 REMARK 500 THR A 130 -64.36 -96.29 REMARK 500 THR A 148 108.08 35.74 REMARK 500 ASP A 181 20.59 -74.52 REMARK 500 ASP A 211 100.89 158.68 REMARK 500 LYS A 230 27.95 -146.31 REMARK 500 LEU A 246 96.47 -48.39 REMARK 500 PRO A 271 110.76 -33.03 REMARK 500 PHE A 285 121.53 -34.44 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 GLY A 49 THR A 50 -148.49 REMARK 500 SER A 209 VAL A 210 -144.86 REMARK 500 VAL A 210 ASP A 211 135.09 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 CU A 357 CU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 108 ND1 REMARK 620 2 HIS A 172 ND1 157.1 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CU A 358 CU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 242 NE2 REMARK 620 2 HIS A 244 NE2 96.7 REMARK 620 3 HOH A 842 O 70.8 66.0 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CU A 360 CU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 279 NE2 REMARK 620 2 HOH A 715 O 167.6 REMARK 620 3 HOH A 778 O 89.3 99.9 REMARK 620 4 HOH A 832 O 92.1 80.0 171.6 REMARK 620 5 HOH A 833 O 97.3 74.0 94.2 93.8 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 CU A 357 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CU A 360 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CU A 361 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CU A 358 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 703 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 710 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1YIP RELATED DB: PDB REMARK 900 RELATED ID: 1PHM RELATED DB: PDB REMARK 900 OXIDIZED PHM STRUCTURE REMARK 900 RELATED ID: 1OPM RELATED DB: PDB REMARK 900 OXIDIZED PHM STRUCTURE WITH SUBSTRATE REMARK 900 RELATED ID: 3PHM RELATED DB: PDB REMARK 900 REDUCED PHM STRUCTURE REMARK 900 RELATED ID: 1SDW RELATED DB: PDB REMARK 900 REDUCED PHM STRUCTURE WITH SUBSTRATE AND DIOXYGEN DBREF 1YI9 A 47 355 UNP P14925 AMD_RAT 47 355 SEQADV 1YI9 ILE A 314 UNP P14925 MET 314 ENGINEERED MUTATION SEQRES 1 A 309 CYS LEU GLY THR ILE GLY PRO VAL THR PRO LEU ASP ALA SEQRES 2 A 309 SER ASP PHE ALA LEU ASP ILE ARG MET PRO GLY VAL THR SEQRES 3 A 309 PRO LYS GLU SER ASP THR TYR PHE CYS MET SER MET ARG SEQRES 4 A 309 LEU PRO VAL ASP GLU GLU ALA PHE VAL ILE ASP PHE LYS SEQRES 5 A 309 PRO ARG ALA SER MET ASP THR VAL HIS HIS MET LEU LEU SEQRES 6 A 309 PHE GLY CYS ASN MET PRO SER SER THR GLY SER TYR TRP SEQRES 7 A 309 PHE CYS ASP GLU GLY THR CYS THR ASP LYS ALA ASN ILE SEQRES 8 A 309 LEU TYR ALA TRP ALA ARG ASN ALA PRO PRO THR ARG LEU SEQRES 9 A 309 PRO LYS GLY VAL GLY PHE ARG VAL GLY GLY GLU THR GLY SEQRES 10 A 309 SER LYS TYR PHE VAL LEU GLN VAL HIS TYR GLY ASP ILE SEQRES 11 A 309 SER ALA PHE ARG ASP ASN HIS LYS ASP CYS SER GLY VAL SEQRES 12 A 309 SER VAL HIS LEU THR ARG VAL PRO GLN PRO LEU ILE ALA SEQRES 13 A 309 GLY MET TYR LEU MET MET SER VAL ASP THR VAL ILE PRO SEQRES 14 A 309 PRO GLY GLU LYS VAL VAL ASN ALA ASP ILE SER CYS GLN SEQRES 15 A 309 TYR LYS MET TYR PRO MET HIS VAL PHE ALA TYR ARG VAL SEQRES 16 A 309 HIS THR HIS HIS LEU GLY LYS VAL VAL SER GLY TYR ARG SEQRES 17 A 309 VAL ARG ASN GLY GLN TRP THR LEU ILE GLY ARG GLN ASN SEQRES 18 A 309 PRO GLN LEU PRO GLN ALA PHE TYR PRO VAL GLU HIS PRO SEQRES 19 A 309 VAL ASP VAL THR PHE GLY ASP ILE LEU ALA ALA ARG CYS SEQRES 20 A 309 VAL PHE THR GLY GLU GLY ARG THR GLU ALA THR HIS ILE SEQRES 21 A 309 GLY GLY THR SER SER ASP GLU ILE CYS ASN LEU TYR ILE SEQRES 22 A 309 MET TYR TYR MET GLU ALA LYS TYR ALA LEU SER PHE MET SEQRES 23 A 309 THR CYS THR LYS ASN VAL ALA PRO ASP MET PHE ARG THR SEQRES 24 A 309 ILE PRO ALA GLU ALA ASN ILE PRO ILE PRO HET CU A 357 1 HET CU A 360 1 HET CU A 361 1 HET CU A 358 1 HET GOL A 703 6 HET GOL A 710 6 HETNAM CU COPPER (II) ION HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 CU 4(CU 2+) FORMUL 6 GOL 2(C3 H8 O3) FORMUL 8 HOH *132(H2 O) HELIX 1 1 ASP A 127 GLY A 129 5 3 HELIX 2 2 LYS A 326 ALA A 328 5 3 HELIX 3 3 ALA A 339 ILE A 346 5 8 HELIX 4 4 PRO A 347 ILE A 352 5 6 SHEET 1 A 9 VAL A 54 PRO A 56 0 SHEET 2 A 9 ASP A 61 ARG A 67 -1 O ALA A 63 N THR A 55 SHEET 3 A 9 GLY A 188 THR A 194 -1 O VAL A 191 N LEU A 64 SHEET 4 A 9 ALA A 92 ARG A 100 -1 N ARG A 100 O GLY A 188 SHEET 5 A 9 VAL A 154 VAL A 158 -1 O PHE A 156 N VAL A 94 SHEET 6 A 9 LEU A 200 SER A 209 1 O ALA A 202 N GLY A 155 SHEET 7 A 9 CYS A 315 GLU A 324 -1 O LEU A 317 N MET A 207 SHEET 8 A 9 MET A 234 THR A 243 -1 N HIS A 242 O ASN A 316 SHEET 9 A 9 TYR A 275 VAL A 283 -1 O TYR A 275 N TYR A 239 SHEET 1 B 7 VAL A 54 PRO A 56 0 SHEET 2 B 7 ASP A 61 ARG A 67 -1 O ALA A 63 N THR A 55 SHEET 3 B 7 GLY A 188 THR A 194 -1 O VAL A 191 N LEU A 64 SHEET 4 B 7 ALA A 92 ARG A 100 -1 N ARG A 100 O GLY A 188 SHEET 5 B 7 VAL A 154 VAL A 158 -1 O PHE A 156 N VAL A 94 SHEET 6 B 7 LEU A 200 SER A 209 1 O ALA A 202 N GLY A 155 SHEET 7 B 7 PHE A 331 CYS A 334 1 O MET A 332 N LEU A 206 SHEET 1 C 5 TRP A 124 PHE A 125 0 SHEET 2 C 5 THR A 78 ARG A 85 -1 N CYS A 81 O TRP A 124 SHEET 3 C 5 TYR A 166 TYR A 173 -1 O TYR A 173 N THR A 78 SHEET 4 C 5 VAL A 106 CYS A 114 -1 N LEU A 110 O GLN A 170 SHEET 5 C 5 ASN A 136 ALA A 142 -1 O LEU A 138 N LEU A 111 SHEET 1 D 4 VAL A 220 GLN A 228 0 SHEET 2 D 4 ILE A 288 THR A 296 -1 O PHE A 295 N VAL A 221 SHEET 3 D 4 GLY A 247 ARG A 256 -1 N VAL A 249 O VAL A 294 SHEET 4 D 4 GLN A 259 GLN A 266 -1 O ILE A 263 N GLY A 252 SSBOND 1 CYS A 47 CYS A 186 1555 1555 2.06 SSBOND 2 CYS A 81 CYS A 126 1555 1555 2.01 SSBOND 3 CYS A 114 CYS A 131 1555 1555 2.06 SSBOND 4 CYS A 227 CYS A 334 1555 1555 2.01 SSBOND 5 CYS A 293 CYS A 315 1555 1555 1.95 LINK ND1 HIS A 108 CU CU A 357 1555 1555 2.00 LINK ND1 HIS A 172 CU CU A 357 1555 1555 2.01 LINK NE2 HIS A 242 CU CU A 358 1555 1555 2.05 LINK NE2 HIS A 244 CU CU A 358 1555 1555 1.97 LINK ND1 HIS A 245 CU CU A 361 1555 1555 2.01 LINK NE2 HIS A 279 CU CU A 360 1555 1555 2.01 LINK CU CU A 358 O HOH A 842 1555 1555 1.92 LINK CU CU A 360 O HOH A 715 1555 1555 2.21 LINK CU CU A 360 O HOH A 778 1555 1555 2.44 LINK CU CU A 360 O HOH A 832 1555 1555 2.24 LINK CU CU A 360 O HOH A 833 1555 1555 2.09 SITE 1 AC1 2 HIS A 108 HIS A 172 SITE 1 AC2 6 GLU A 128 HIS A 279 HOH A 715 HOH A 778 SITE 2 AC2 6 HOH A 832 HOH A 833 SITE 1 AC3 3 HIS A 245 GLU A 313 HOH A 838 SITE 1 AC4 3 HIS A 242 HIS A 244 HOH A 842 SITE 1 AC5 7 TYR A 205 GLN A 228 TYR A 229 LYS A 230 SITE 2 AC5 7 MET A 231 MET A 332 HOH A 789 SITE 1 AC6 6 LYS A 219 TYR A 253 LEU A 262 ARG A 265 SITE 2 AC6 6 PRO A 347 GLU A 349 CRYST1 59.479 66.458 70.049 90.00 90.00 90.00 P 21 21 21 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 0.016813 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015047 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014276 0.00000 MASTER 442 0 6 4 25 0 9 6 0 0 0 24 END