HEADER OXIDOREDUCTASE 17-MAR-15 4YSP TITLE STRUCTURE OF COPPER NITRITE REDUCTASE FROM GEOBACILLUS TITLE 2 THERMODENITRIFICANS - 8.32 MGY COMPND MOL_ID: 1; COMPND 2 MOLECULE: NITRITE REDUCTASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 31-352; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: GEOBACILLUS THERMODENITRIFICANS (STRAIN NG80- SOURCE 3 2); SOURCE 4 ORGANISM_TAXID: 420246; SOURCE 5 STRAIN: NG80-2; SOURCE 6 GENE: NIRK, GTNG_0650; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET22B KEYWDS NITRITE, COPPER, REDUCTASE, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR Y.FUKUDA,K.M.TSE,M.SUZUKI,K.DIEDRICHS,K.HIRATA,T.NAKANE,M.SUGAHARA, AUTHOR 2 E.NANGO,K.TONO,Y.JOTI,T.KAMESHIMA,C.SONG,T.HATSUI,M.YABASHI, AUTHOR 3 O.NUREKI,H.MATSUMURA,T.INOUE,S.IWATA,E.MIZOHATA REVDAT 4 20-MAR-24 4YSP 1 LINK REVDAT 3 05-FEB-20 4YSP 1 REMARK REVDAT 2 25-MAY-16 4YSP 1 JRNL REVDAT 1 24-FEB-16 4YSP 0 JRNL AUTH Y.FUKUDA,K.M.TSE,M.SUZUKI,K.DIEDERICHS,K.HIRATA,T.NAKANE, JRNL AUTH 2 M.SUGAHARA,E.NANGO,K.TONO,Y.JOTI,T.KAMESHIMA,C.SONG, JRNL AUTH 3 T.HATSUI,M.YABASHI,O.NUREKI,H.MATSUMURA,T.INOUE,S.IWATA, JRNL AUTH 4 E.MIZOHATA JRNL TITL REDOX-COUPLED STRUCTURAL CHANGES IN NITRITE REDUCTASE JRNL TITL 2 REVEALED BY SERIAL FEMTOSECOND AND MICROFOCUS JRNL TITL 3 CRYSTALLOGRAPHY JRNL REF J.BIOCHEM. V. 159 527 2016 JRNL REFN ISSN 0021-924X JRNL PMID 26769972 JRNL DOI 10.1093/JB/MVV133 REMARK 2 REMARK 2 RESOLUTION. 1.34 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0049 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) : 1.34 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.08 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 93.5 REMARK 3 NUMBER OF REFLECTIONS : 83461 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) : 0.126 REMARK 3 R VALUE (WORKING SET) : 0.124 REMARK 3 FREE R VALUE : 0.150 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 4443 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) : 1.34 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.37 REMARK 3 REFLECTION IN BIN (WORKING SET) : 6382 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.49 REMARK 3 BIN R VALUE (WORKING SET) : 0.1470 REMARK 3 BIN FREE R VALUE SET COUNT : 335 REMARK 3 BIN FREE R VALUE : 0.1880 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2293 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 20 REMARK 3 SOLVENT ATOMS : 285 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 13.57 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.03000 REMARK 3 B22 (A**2) : -0.03000 REMARK 3 B33 (A**2) : 0.09000 REMARK 3 B12 (A**2) : -0.01000 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): 0.037 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.037 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.021 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.121 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.967 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.958 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2469 ; 0.022 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 2335 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3378 ; 2.079 ; 1.950 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5401 ; 0.926 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 315 ; 8.186 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 107 ;43.581 ;25.421 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 403 ;11.736 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 4 ; 8.340 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 370 ; 0.143 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2851 ; 0.012 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 551 ; 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): 1233 ; 1.512 ; 1.076 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1232 ; 1.459 ; 1.074 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1557 ; 1.722 ; 1.623 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1558 ; 1.724 ; 1.625 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1236 ; 2.762 ; 1.325 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1233 ; 2.659 ; 1.319 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 1816 ; 2.704 ; 1.875 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 2847 ; 2.855 ;10.091 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 2718 ; 2.593 ; 9.430 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): 4804 ; 5.644 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 95 ;21.948 ; 5.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 4936 ; 7.256 ; 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 4YSP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 19-MAR-15. REMARK 100 THE DEPOSITION ID IS D_1000208041. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-APR-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.5 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL32XU REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.75000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX225HE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 87908 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.340 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.6 REMARK 200 DATA REDUNDANCY : 3.100 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 59.16 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.01 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M SODIUM ACETATE, 5.5%(W/V) PEG REMARK 280 4000, 0.075M CUSO4, PH 4.5, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H 3 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 X+2/3,Y+1/3,Z+1/3 REMARK 290 5555 -Y+2/3,X-Y+1/3,Z+1/3 REMARK 290 6555 -X+Y+2/3,-X+1/3,Z+1/3 REMARK 290 7555 X+1/3,Y+2/3,Z+2/3 REMARK 290 8555 -Y+1/3,X-Y+2/3,Z+2/3 REMARK 290 9555 -X+Y+1/3,-X+2/3,Z+2/3 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 57.44800 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 33.16762 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 28.07767 REMARK 290 SMTRY1 5 -0.500000 -0.866025 0.000000 57.44800 REMARK 290 SMTRY2 5 0.866025 -0.500000 0.000000 33.16762 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 28.07767 REMARK 290 SMTRY1 6 -0.500000 0.866025 0.000000 57.44800 REMARK 290 SMTRY2 6 -0.866025 -0.500000 0.000000 33.16762 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 28.07767 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 66.33524 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 56.15533 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 66.33524 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 56.15533 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 66.33524 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 56.15533 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 12110 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 28360 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -257.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 3 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 MET A 1 REMARK 465 GLU A 2 REMARK 465 SER A 3 REMARK 465 LYS A 4 REMARK 465 ASN A 5 REMARK 465 LYS A 6 REMARK 465 THR A 7 REMARK 465 ALA A 8 REMARK 465 ALA A 9 REMARK 465 THR A 10 REMARK 465 GLN A 11 REMARK 465 GLN A 12 REMARK 465 SER A 13 REMARK 465 GLU A 14 REMARK 465 PRO A 15 REMARK 465 ASN A 16 REMARK 465 VAL A 17 REMARK 465 GLY A 313 REMARK 465 GLU A 314 REMARK 465 ASP A 315 REMARK 465 ASP A 316 REMARK 465 GLY A 317 REMARK 465 THR A 318 REMARK 465 GLU A 319 REMARK 465 THR A 320 REMARK 465 SER A 321 REMARK 465 GLY A 322 REMARK 465 HIS A 323 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 168 NE - CZ - NH1 ANGL. DEV. = -3.7 DEGREES REMARK 500 ARG A 168 NE - CZ - NH2 ANGL. DEV. = 3.5 DEGREES REMARK 500 PHE A 186 CB - CG - CD1 ANGL. DEV. = 4.4 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 PRO A 70 163.43 -47.92 REMARK 500 PHE A 213 -30.95 -134.75 REMARK 500 SER A 242 77.95 -112.33 REMARK 500 ASP A 256 12.77 59.24 REMARK 500 ASN A 261 56.98 -94.22 REMARK 500 SER A 274 -1.93 82.91 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 VAL A 292 THR A 293 147.53 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 785 DISTANCE = 6.04 ANGSTROMS 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 403 CU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 42 NE2 REMARK 620 2 GLU A 53 OE2 44.5 REMARK 620 3 HIS A 83 ND1 108.0 81.0 REMARK 620 4 HOH A 567 O 165.6 149.8 81.6 REMARK 620 5 HOH A 725 O 99.9 72.0 102.6 88.1 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CU A 401 CU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 95 ND1 REMARK 620 2 CYS A 135 SG 134.2 REMARK 620 3 HIS A 143 ND1 104.2 106.9 REMARK 620 4 MET A 148 SD 81.5 112.1 116.8 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CU A 402 CU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 100 NE2 REMARK 620 2 HIS A 134 NE2 114.1 REMARK 620 3 HIS A 294 NE2 71.1 103.9 REMARK 620 4 HOH A 724 O 127.5 105.5 130.8 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CU A 406 CU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 103 NE2 REMARK 620 2 THR A 248 OG1 118.5 REMARK 620 3 VAL A 249 N 123.0 4.9 REMARK 620 4 VAL A 249 O 120.3 4.3 3.5 REMARK 620 5 HOH A 520 O 116.5 5.4 7.3 3.9 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CU A 407 CU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 239 OE2 REMARK 620 2 HOH A 540 O 87.2 REMARK 620 3 HOH A 563 O 99.6 114.4 REMARK 620 N 1 2 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 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CU A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CU A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CU A 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CU A 405 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CU A 406 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CU A 407 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MPD A 408 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 409 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4YSA RELATED DB: PDB REMARK 900 RELATED ID: 4YSC RELATED DB: PDB REMARK 900 RELATED ID: 4YSD RELATED DB: PDB REMARK 900 RELATED ID: 4YSE RELATED DB: PDB REMARK 900 RELATED ID: 4YSO RELATED DB: PDB REMARK 900 RELATED ID: 4YSQ RELATED DB: PDB REMARK 900 RELATED ID: 4YSR RELATED DB: PDB REMARK 900 RELATED ID: 4YSS RELATED DB: PDB REMARK 900 RELATED ID: 4YST RELATED DB: PDB REMARK 900 RELATED ID: 4YSU RELATED DB: PDB DBREF 4YSP A 2 323 UNP A4IL26 A4IL26_GEOTN 31 352 SEQADV 4YSP MET A 1 UNP A4IL26 INITIATING METHIONINE SEQRES 1 A 323 MET GLU SER LYS ASN LYS THR ALA ALA THR GLN GLN SER SEQRES 2 A 323 GLU PRO ASN VAL ILE ALA ALA HIS LYS GLY VAL ASN GLN SEQRES 3 A 323 ALA PRO VAL PRO LEU LYS MET GLU ARG VAL GLY PRO HIS SEQRES 4 A 323 ASP VAL HIS ILE GLU MET THR ALA GLN ILE THR ASP ILE SEQRES 5 A 323 GLU ILE ASP LYS GLY LYS ILE TYR LYS ALA TRP THR PHE SEQRES 6 A 323 ASN GLY GLN ALA PRO GLY PRO LEU VAL VAL VAL ASN GLU SEQRES 7 A 323 GLY ASP THR ILE HIS PHE THR LEU LYS ASN MET ASP PRO SEQRES 8 A 323 VAL VAL PRO HIS SER MET ASP PHE HIS ALA VAL HIS ALA SEQRES 9 A 323 SER PRO SER LYS ASP PHE ILE ASP VAL MET PRO ASN LYS SEQRES 10 A 323 SER GLY THR PHE THR TYR PRO ALA ASN LYS PRO GLY VAL SEQRES 11 A 323 PHE MET TYR HIS CYS GLY THR LYS PRO VAL LEU GLN HIS SEQRES 12 A 323 ILE ALA ASN GLY MET HIS GLY VAL ILE ILE VAL LYS PRO SEQRES 13 A 323 LYS ASN GLY TYR PRO THR ASP LYS GLU VAL ASP ARG GLU SEQRES 14 A 323 TYR VAL LEU ILE GLN ASN GLU TRP TYR LYS TYR ASN ASP SEQRES 15 A 323 MET ASN ASP PHE GLN ASN GLY VAL PRO SER TYR VAL VAL SEQRES 16 A 323 PHE SER SER LYS ALA LEU LYS PRO GLY ASP PRO ASN THR SEQRES 17 A 323 ASN GLY ASP THR PHE THR LEU LYS GLU LYS PRO LEU LEU SEQRES 18 A 323 ALA LYS VAL GLY GLU LYS ILE ARG LEU TYR ILE ASN ASN SEQRES 19 A 323 VAL GLY PRO ASN GLU VAL SER SER PHE HIS VAL VAL GLY SEQRES 20 A 323 THR VAL PHE ASP ASP VAL TYR LEU ASP GLY ASN PRO ASN SEQRES 21 A 323 ASN HIS LEU GLN GLY MET GLN THR VAL MET LEU PRO ALA SEQRES 22 A 323 SER GLY GLY ALA VAL VAL GLU PHE THR VAL THR ARG PRO SEQRES 23 A 323 GLY THR TYR PRO ILE VAL THR HIS GLN PHE ASN HIS ALA SEQRES 24 A 323 GLN LYS GLY ALA VAL ALA MET LEU LYS VAL THR GLU THR SEQRES 25 A 323 GLY GLU ASP ASP GLY THR GLU THR SER GLY HIS HET CU A 401 1 HET CU A 402 1 HET CU A 403 1 HET CU A 404 1 HET CU A 405 1 HET CU A 406 1 HET CU A 407 1 HET MPD A 408 8 HET SO4 A 409 5 HETNAM CU COPPER (II) ION HETNAM MPD (4S)-2-METHYL-2,4-PENTANEDIOL HETNAM SO4 SULFATE ION FORMUL 2 CU 7(CU 2+) FORMUL 9 MPD C6 H14 O2 FORMUL 10 SO4 O4 S 2- FORMUL 11 HOH *285(H2 O) HELIX 1 AA1 ILE A 18 LYS A 22 5 5 HELIX 2 AA2 SER A 105 PHE A 110 1 6 HELIX 3 AA3 PRO A 139 ASN A 146 1 8 HELIX 4 AA4 THR A 162 VAL A 166 5 5 HELIX 5 AA5 ASP A 182 GLY A 189 1 8 HELIX 6 AA6 PHE A 213 LYS A 218 1 6 HELIX 7 AA7 GLN A 295 LYS A 301 1 7 SHEET 1 AA1 3 LYS A 32 GLY A 37 0 SHEET 2 AA1 3 ASP A 40 ASP A 55 -1 O HIS A 42 N GLU A 34 SHEET 3 AA1 3 LYS A 58 PHE A 65 -1 O TYR A 60 N ILE A 52 SHEET 1 AA2 4 LYS A 32 GLY A 37 0 SHEET 2 AA2 4 ASP A 40 ASP A 55 -1 O HIS A 42 N GLU A 34 SHEET 3 AA2 4 ASP A 80 ASN A 88 1 O THR A 85 N MET A 45 SHEET 4 AA2 4 SER A 118 ALA A 125 -1 O PHE A 121 N PHE A 84 SHEET 1 AA3 4 VAL A 74 ASN A 77 0 SHEET 2 AA3 4 HIS A 149 LYS A 155 1 O LYS A 155 N VAL A 76 SHEET 3 AA3 4 GLY A 129 HIS A 134 -1 N GLY A 129 O VAL A 154 SHEET 4 AA3 4 ASP A 98 PHE A 99 -1 N ASP A 98 O HIS A 134 SHEET 1 AA4 6 TYR A 193 LYS A 199 0 SHEET 2 AA4 6 ARG A 168 TRP A 177 -1 N ASN A 175 O VAL A 195 SHEET 3 AA4 6 LYS A 227 GLY A 236 1 O ARG A 229 N ARG A 168 SHEET 4 AA4 6 GLY A 276 THR A 282 -1 O PHE A 281 N ILE A 228 SHEET 5 AA4 6 PHE A 250 LEU A 255 -1 N TYR A 254 O VAL A 278 SHEET 6 AA4 6 HIS A 262 MET A 266 -1 O MET A 266 N PHE A 250 SHEET 1 AA5 5 LEU A 220 LYS A 223 0 SHEET 2 AA5 5 VAL A 304 THR A 310 1 O LYS A 308 N LEU A 220 SHEET 3 AA5 5 GLY A 287 THR A 293 -1 N GLY A 287 O VAL A 309 SHEET 4 AA5 5 SER A 241 VAL A 245 -1 N HIS A 244 O VAL A 292 SHEET 5 AA5 5 VAL A 269 LEU A 271 -1 O LEU A 271 N SER A 241 LINK NE2 HIS A 39 CU CU A 404 1555 1555 1.94 LINK NE2 HIS A 42 CU CU A 403 1555 1555 2.07 LINK OE2 GLU A 53 CU CU A 403 1555 8554 1.99 LINK ND1 HIS A 83 CU CU A 403 1555 1555 1.98 LINK ND1 HIS A 95 CU CU A 401 1555 1555 2.04 LINK NE2 HIS A 100 CU CU A 402 1555 1555 2.05 LINK NE2 HIS A 103 CU CU A 406 1555 2555 2.37 LINK NE2 HIS A 134 CU CU A 402 1555 1555 2.02 LINK SG CYS A 135 CU CU A 401 1555 1555 2.23 LINK ND1 HIS A 143 CU CU A 401 1555 1555 2.05 LINK SD MET A 148 CU CU A 401 1555 1555 2.64 LINK OD2 ASP A 167 CU CU A 405 1555 1555 2.10 LINK OE2 GLU A 239 CU CU A 407 1555 1555 2.31 LINK OG1 THR A 248 CU CU A 406 1555 1555 2.18 LINK N VAL A 249 CU CU A 406 1555 1555 2.08 LINK O VAL A 249 CU CU A 406 1555 1555 2.05 LINK NE2 HIS A 294 CU CU A 402 1555 3555 1.99 LINK CU CU A 402 O HOH A 724 1555 1555 2.27 LINK CU CU A 403 O HOH A 567 1555 6455 2.62 LINK CU CU A 403 O HOH A 725 1555 1555 2.42 LINK CU CU A 406 O HOH A 520 1555 1555 2.07 LINK CU CU A 407 O HOH A 540 1555 1555 2.64 LINK CU CU A 407 O HOH A 563 1555 1555 1.88 CISPEP 1 ALA A 69 PRO A 70 0 -16.83 CISPEP 2 LYS A 138 PRO A 139 0 -14.01 CISPEP 3 LYS A 138 PRO A 139 0 -2.86 CISPEP 4 GLY A 236 PRO A 237 0 19.99 SITE 1 AC1 4 HIS A 95 CYS A 135 HIS A 143 MET A 148 SITE 1 AC2 4 HIS A 100 HIS A 134 HIS A 294 HOH A 724 SITE 1 AC3 5 HIS A 42 GLU A 53 HIS A 83 HOH A 567 SITE 2 AC3 5 HOH A 725 SITE 1 AC4 1 HIS A 39 SITE 1 AC5 1 ASP A 167 SITE 1 AC6 4 HIS A 103 THR A 248 VAL A 249 HOH A 520 SITE 1 AC7 4 PRO A 191 GLU A 239 HOH A 540 HOH A 563 SITE 1 AC8 5 ASP A 163 ASP A 167 ARG A 168 GLU A 169 SITE 2 AC8 5 HOH A 546 SITE 1 AC9 4 TYR A 193 GLN A 300 LYS A 301 HOH A 600 CRYST1 114.896 114.896 84.233 90.00 90.00 120.00 H 3 9 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 0.008704 0.005025 0.000000 0.00000 SCALE2 0.000000 0.010050 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011872 0.00000