HEADER ELECTRON TRANSPORT 26-FEB-13 3ZOX TITLE CRYSTAL STRUCTURE OF N64DEL MUTANT OF NITROSOMONAS EUROPAEA CYTOCHROME TITLE 2 C552 (MONOCLINIC SPACE GROUP) COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYTOCHROME C-552; COMPND 3 CHAIN: A, B, C, D; COMPND 4 SYNONYM: CYTOCHROME C-551, CYTOCHROME C552; COMPND 5 EC: 1.7.2.2; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: NITROSOMONAS EUROPAEA; SOURCE 3 ORGANISM_TAXID: 915; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PSNEC KEYWDS HEMEPROTEIN, ELECTRON TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR H.-P.HERSLETH,M.CAN,J.KRUCINSKA,G.ZOPPELLARO,N.H.ANDERSEN, AUTHOR 2 J.E.WEDEKIND,K.K.ANDERSSON,K.L.BREN REVDAT 4 20-NOV-24 3ZOX 1 REMARK REVDAT 3 20-DEC-23 3ZOX 1 REMARK LINK REVDAT 2 16-OCT-13 3ZOX 1 JRNL REVDAT 1 14-AUG-13 3ZOX 0 JRNL AUTH M.CAN,J.KRUCINSKA,G.ZOPPELLARO,N.H.ANDERSEN,J.E.WEDEKIND, JRNL AUTH 2 H.-P.HERSLETH,K.K.ANDERSSON,K.L.BREN JRNL TITL STRUCTURAL CHARACTERIZATION OF NITROSOMONAS EUROPAEA JRNL TITL 2 CYTOCHROME C-552 VARIANTS WITH MARKED DIFFERENCES IN JRNL TITL 3 ELECTRONIC STRUCTURE. JRNL REF CHEMBIOCHEM V. 14 1828 2013 JRNL REFN ISSN 1439-4227 JRNL PMID 23908017 JRNL DOI 10.1002/CBIC.201300118 REMARK 2 REMARK 2 RESOLUTION. 2.10 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) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.84 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 94.1 REMARK 3 NUMBER OF REFLECTIONS : 23614 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) : 0.215 REMARK 3 R VALUE (WORKING SET) : 0.212 REMARK 3 FREE R VALUE : 0.274 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1273 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) : 2.10 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.16 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1729 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 93.98 REMARK 3 BIN R VALUE (WORKING SET) : 0.2380 REMARK 3 BIN FREE R VALUE SET COUNT : 96 REMARK 3 BIN FREE R VALUE : 0.2890 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2348 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 172 REMARK 3 SOLVENT ATOMS : 160 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.22 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.45000 REMARK 3 B22 (A**2) : -0.30000 REMARK 3 B33 (A**2) : -0.12000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.05000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.211 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.202 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.141 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 10.211 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.920 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.879 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2604 ; 0.025 ; 0.044 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3572 ; 1.983 ; 3.073 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 316 ; 6.882 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 80 ;41.409 ;27.500 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 408 ;16.677 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 376 ; 0.130 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1928 ; 0.010 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL 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): 1276 ; 1.661 ; 1.743 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1588 ; 2.670 ; 2.597 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1327 ; 1.708 ; 1.814 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NCS TYPE: LOCAL REMARK 3 NUMBER OF DIFFERENT NCS PAIRS : 6 REMARK 3 GROUP CHAIN1 RANGE CHAIN2 RANGE COUNT RMS WEIGHT REMARK 3 1 A 1 81 B 1 81 90 0.13 0.05 REMARK 3 2 A 1 81 C 1 81 85 0.14 0.05 REMARK 3 3 A 1 81 D 1 81 82 0.17 0.05 REMARK 3 4 B 1 81 C 1 81 88 0.20 0.05 REMARK 3 5 B 1 81 D 1 81 83 0.15 0.05 REMARK 3 6 C 1 81 D 1 81 85 0.13 0.05 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 8 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 1 A 81 REMARK 3 ORIGIN FOR THE GROUP (A): -17.6530 3.8840 -13.5350 REMARK 3 T TENSOR REMARK 3 T11: 0.0730 T22: 0.0254 REMARK 3 T33: 0.0200 T12: -0.0111 REMARK 3 T13: 0.0038 T23: 0.0064 REMARK 3 L TENSOR REMARK 3 L11: 2.0290 L22: 0.9022 REMARK 3 L33: 3.2524 L12: 0.4767 REMARK 3 L13: -0.3567 L23: 0.2836 REMARK 3 S TENSOR REMARK 3 S11: 0.1172 S12: -0.1568 S13: -0.0249 REMARK 3 S21: 0.0187 S22: 0.0050 S23: -0.0624 REMARK 3 S31: 0.2516 S32: 0.0545 S33: -0.1223 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 1082 A 1082 REMARK 3 ORIGIN FOR THE GROUP (A): -18.6220 1.4830 -18.1980 REMARK 3 T TENSOR REMARK 3 T11: 0.0863 T22: 0.0609 REMARK 3 T33: 0.0170 T12: -0.0358 REMARK 3 T13: -0.0082 T23: 0.0157 REMARK 3 L TENSOR REMARK 3 L11: 1.7094 L22: 6.2605 REMARK 3 L33: 0.4588 L12: 3.2028 REMARK 3 L13: -0.3658 L23: -0.4109 REMARK 3 S TENSOR REMARK 3 S11: -0.0365 S12: 0.1093 S13: 0.1273 REMARK 3 S21: 0.0729 S22: 0.1038 S23: 0.2269 REMARK 3 S31: 0.1366 S32: -0.1484 S33: -0.0673 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 1 B 81 REMARK 3 ORIGIN FOR THE GROUP (A): -31.2280 14.0830 -29.8200 REMARK 3 T TENSOR REMARK 3 T11: 0.0665 T22: 0.0344 REMARK 3 T33: 0.0274 T12: 0.0010 REMARK 3 T13: 0.0146 T23: 0.0171 REMARK 3 L TENSOR REMARK 3 L11: 0.6445 L22: 1.9822 REMARK 3 L33: 3.4224 L12: 0.0098 REMARK 3 L13: -0.3784 L23: -0.2685 REMARK 3 S TENSOR REMARK 3 S11: 0.0801 S12: -0.0013 S13: 0.0090 REMARK 3 S21: -0.0933 S22: 0.0609 S23: 0.0764 REMARK 3 S31: -0.0278 S32: -0.1892 S33: -0.1409 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 1082 B 1082 REMARK 3 ORIGIN FOR THE GROUP (A): -33.3530 11.1050 -25.9450 REMARK 3 T TENSOR REMARK 3 T11: 0.0625 T22: 0.0428 REMARK 3 T33: 0.0221 T12: 0.0243 REMARK 3 T13: -0.0112 T23: 0.0013 REMARK 3 L TENSOR REMARK 3 L11: 0.0778 L22: 3.5482 REMARK 3 L33: 3.8635 L12: 0.1665 REMARK 3 L13: 0.4325 L23: 2.8168 REMARK 3 S TENSOR REMARK 3 S11: -0.0574 S12: -0.0265 S13: 0.0152 REMARK 3 S21: -0.1745 S22: -0.1433 S23: 0.2301 REMARK 3 S31: -0.2521 S32: -0.1950 S33: 0.2007 REMARK 3 REMARK 3 TLS GROUP : 5 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : C 1 C 81 REMARK 3 ORIGIN FOR THE GROUP (A): -36.2540 26.5450 -9.3940 REMARK 3 T TENSOR REMARK 3 T11: 0.0885 T22: 0.0196 REMARK 3 T33: 0.0160 T12: 0.0064 REMARK 3 T13: 0.0330 T23: -0.0034 REMARK 3 L TENSOR REMARK 3 L11: 0.7024 L22: 3.0805 REMARK 3 L33: 2.9796 L12: -0.6083 REMARK 3 L13: -0.1538 L23: -0.1287 REMARK 3 S TENSOR REMARK 3 S11: 0.0165 S12: -0.0389 S13: 0.0150 REMARK 3 S21: 0.0942 S22: 0.0752 S23: -0.0399 REMARK 3 S31: -0.0879 S32: 0.0908 S33: -0.0918 REMARK 3 REMARK 3 TLS GROUP : 6 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : C 1082 C 1082 REMARK 3 ORIGIN FOR THE GROUP (A): -35.8210 29.4580 -13.7470 REMARK 3 T TENSOR REMARK 3 T11: 0.1100 T22: 0.0778 REMARK 3 T33: 0.0714 T12: -0.0222 REMARK 3 T13: -0.0048 T23: 0.0585 REMARK 3 L TENSOR REMARK 3 L11: 0.1369 L22: 0.7658 REMARK 3 L33: 2.6991 L12: 0.2625 REMARK 3 L13: -0.5117 L23: -1.3884 REMARK 3 S TENSOR REMARK 3 S11: -0.0733 S12: -0.0088 S13: -0.0442 REMARK 3 S21: 0.0289 S22: -0.1246 S23: -0.1559 REMARK 3 S31: -0.0429 S32: 0.0928 S33: 0.1979 REMARK 3 REMARK 3 TLS GROUP : 7 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : D 1 D 81 REMARK 3 ORIGIN FOR THE GROUP (A): -1.7630 10.1430 -30.8960 REMARK 3 T TENSOR REMARK 3 T11: 0.0692 T22: 0.0888 REMARK 3 T33: 0.0168 T12: -0.0094 REMARK 3 T13: 0.0279 T23: -0.0080 REMARK 3 L TENSOR REMARK 3 L11: 2.9446 L22: 0.8731 REMARK 3 L33: 2.9314 L12: 0.5004 REMARK 3 L13: 0.7741 L23: 0.9010 REMARK 3 S TENSOR REMARK 3 S11: -0.0080 S12: 0.1161 S13: -0.0008 REMARK 3 S21: -0.0824 S22: 0.0986 S23: 0.0008 REMARK 3 S31: -0.0872 S32: 0.2947 S33: -0.0907 REMARK 3 REMARK 3 TLS GROUP : 8 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : D 1082 D 1082 REMARK 3 ORIGIN FOR THE GROUP (A): -0.0310 10.9330 -25.8900 REMARK 3 T TENSOR REMARK 3 T11: 0.0523 T22: 0.0559 REMARK 3 T33: 0.0975 T12: -0.0228 REMARK 3 T13: -0.0114 T23: 0.0090 REMARK 3 L TENSOR REMARK 3 L11: 8.1099 L22: 0.2832 REMARK 3 L33: 3.5968 L12: -1.3941 REMARK 3 L13: -3.3014 L23: 0.3086 REMARK 3 S TENSOR REMARK 3 S11: -0.2755 S12: -0.0529 S13: 0.2116 REMARK 3 S21: 0.0618 S22: -0.0316 S23: -0.0823 REMARK 3 S31: -0.0340 S32: 0.1581 S33: 0.3071 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. HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT IT REMARK 3 IS COMMON IN PUBLICATIONS ETC. TO START THE NUMBERING OF THE REMARK 3 CYTOCHROME C552 NITROSOMONAS EUROPAEA WITH THE FIRST RESIDUE IN REMARK 3 THE SEQUENCE BEING NUMBERED AS RESIDUE 3. THEREFORE THE N62DEL REMARK 3 MUTANT IS NORMALLY REFERRED TO AS N64DEL. SINGLE-CRYSTAL UV-VIS REMARK 3 SPECTRA HAVE BEEN RECORDED BEFORE AND AFTER EXPOSURE TO X-RAYS REMARK 3 SHOWING THE RADIATION-INFLUENCE OF THE FERRIC CYTOCHROME C552 REMARK 3 CRYSTALS SEE JRNL. REMARK 4 REMARK 4 3ZOX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 26-FEB-13. REMARK 100 THE DEPOSITION ID IS D_1290055971. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-APR-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 9.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID29 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9760 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 24887 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 40.800 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 6.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.3 REMARK 200 DATA REDUNDANCY : 2.400 REMARK 200 R MERGE (I) : 0.15000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 4.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.20 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.0 REMARK 200 DATA REDUNDANCY IN SHELL : 2.40 REMARK 200 R MERGE FOR SHELL (I) : 0.50000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 351C REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 59.50 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.06 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M CHES PH 9.5, 30% (W/V) PEG 8000 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 69.26000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 40.62000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 69.26000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 40.62000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3, 4 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 350 REMARK 350 BIOMOLECULE: 3 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: C 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: 4 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: D 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 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 HOH D 2001 O HOH D 2023 1.94 REMARK 500 O HOH B 2001 O HOH B 2042 2.07 REMARK 500 O HOH D 2025 O HOH D 2026 2.11 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 ND2 ASN D 9 NE2 GLN D 56 2554 2.16 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 VAL A 20 -87.84 -101.66 REMARK 500 LEU A 80 21.97 -78.78 REMARK 500 ASN B 9 -2.24 73.44 REMARK 500 VAL B 20 -90.33 -103.61 REMARK 500 VAL C 20 -89.81 -111.63 REMARK 500 VAL D 20 -85.60 -112.01 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 HEC A1082 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 14 NE2 REMARK 620 2 HEC A1082 NA 90.3 REMARK 620 3 HEC A1082 NB 91.3 95.7 REMARK 620 4 HEC A1082 NC 90.5 178.1 82.6 REMARK 620 5 HEC A1082 ND 88.3 88.5 175.7 93.2 REMARK 620 6 MET A 59 SD 175.4 85.4 90.7 93.9 90.0 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HEC B1082 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 14 NE2 REMARK 620 2 HEC B1082 NA 90.8 REMARK 620 3 HEC B1082 NB 94.5 92.9 REMARK 620 4 HEC B1082 NC 91.7 175.0 82.6 REMARK 620 5 HEC B1082 ND 86.3 88.4 178.5 96.1 REMARK 620 6 MET B 59 SD 172.5 81.8 87.1 95.7 92.3 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HEC C1082 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS C 14 NE2 REMARK 620 2 HEC C1082 NA 90.8 REMARK 620 3 HEC C1082 NB 92.7 87.0 REMARK 620 4 HEC C1082 NC 86.3 175.4 96.7 REMARK 620 5 HEC C1082 ND 87.7 94.1 178.8 82.2 REMARK 620 6 MET C 59 SD 172.3 83.3 92.0 99.2 87.8 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HEC D1082 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS D 14 NE2 REMARK 620 2 HEC D1082 NA 85.2 REMARK 620 3 HEC D1082 NB 91.2 87.7 REMARK 620 4 HEC D1082 NC 94.3 175.6 87.9 REMARK 620 5 HEC D1082 ND 87.8 91.9 179.0 92.4 REMARK 620 6 MET D 59 SD 172.8 87.9 90.7 92.7 90.2 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 HEC A 1082 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HEC B 1082 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HEC C 1082 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HEC D 1082 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3ZOW RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF WILD TYPE NITROSOMONAS EUROPAEA CYTOCHROME C552 REMARK 900 RELATED ID: 3ZOY RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF N64DEL MUTANT OF NITROSOMONAS EUROPAEA REMARK 900 CYTOCHROME C552 (HEXAGONAL SPACE GROUP) REMARK 900 RELATED ID: 4JCG RELATED DB: PDB DBREF 3ZOX A 1 81 UNP P95339 CY552_NITEU 23 103 DBREF 3ZOX B 1 81 UNP P95339 CY552_NITEU 23 103 DBREF 3ZOX C 1 81 UNP P95339 CY552_NITEU 23 103 DBREF 3ZOX D 1 81 UNP P95339 CY552_NITEU 23 103 SEQADV 3ZOX A UNP P95339 ASN 84 DELETION SEQADV 3ZOX B UNP P95339 ASN 84 DELETION SEQADV 3ZOX C UNP P95339 ASN 84 DELETION SEQADV 3ZOX D UNP P95339 ASN 84 DELETION SEQRES 1 A 80 ASP ALA ASP LEU ALA LYS LYS ASN ASN CYS ILE ALA CYS SEQRES 2 A 80 HIS GLN VAL GLU THR LYS VAL VAL GLY PRO ALA LEU LYS SEQRES 3 A 80 ASP ILE ALA ALA LYS TYR ALA ASP LYS ASP ASP ALA ALA SEQRES 4 A 80 THR TYR LEU ALA GLY LYS ILE LYS GLY GLY SER SER GLY SEQRES 5 A 80 VAL TRP GLY GLN ILE PRO MET PRO PRO VAL ASN VAL SER SEQRES 6 A 80 ASP ALA ASP ALA LYS ALA LEU ALA ASP TRP ILE LEU THR SEQRES 7 A 80 LEU LYS SEQRES 1 B 80 ASP ALA ASP LEU ALA LYS LYS ASN ASN CYS ILE ALA CYS SEQRES 2 B 80 HIS GLN VAL GLU THR LYS VAL VAL GLY PRO ALA LEU LYS SEQRES 3 B 80 ASP ILE ALA ALA LYS TYR ALA ASP LYS ASP ASP ALA ALA SEQRES 4 B 80 THR TYR LEU ALA GLY LYS ILE LYS GLY GLY SER SER GLY SEQRES 5 B 80 VAL TRP GLY GLN ILE PRO MET PRO PRO VAL ASN VAL SER SEQRES 6 B 80 ASP ALA ASP ALA LYS ALA LEU ALA ASP TRP ILE LEU THR SEQRES 7 B 80 LEU LYS SEQRES 1 C 80 ASP ALA ASP LEU ALA LYS LYS ASN ASN CYS ILE ALA CYS SEQRES 2 C 80 HIS GLN VAL GLU THR LYS VAL VAL GLY PRO ALA LEU LYS SEQRES 3 C 80 ASP ILE ALA ALA LYS TYR ALA ASP LYS ASP ASP ALA ALA SEQRES 4 C 80 THR TYR LEU ALA GLY LYS ILE LYS GLY GLY SER SER GLY SEQRES 5 C 80 VAL TRP GLY GLN ILE PRO MET PRO PRO VAL ASN VAL SER SEQRES 6 C 80 ASP ALA ASP ALA LYS ALA LEU ALA ASP TRP ILE LEU THR SEQRES 7 C 80 LEU LYS SEQRES 1 D 80 ASP ALA ASP LEU ALA LYS LYS ASN ASN CYS ILE ALA CYS SEQRES 2 D 80 HIS GLN VAL GLU THR LYS VAL VAL GLY PRO ALA LEU LYS SEQRES 3 D 80 ASP ILE ALA ALA LYS TYR ALA ASP LYS ASP ASP ALA ALA SEQRES 4 D 80 THR TYR LEU ALA GLY LYS ILE LYS GLY GLY SER SER GLY SEQRES 5 D 80 VAL TRP GLY GLN ILE PRO MET PRO PRO VAL ASN VAL SER SEQRES 6 D 80 ASP ALA ASP ALA LYS ALA LEU ALA ASP TRP ILE LEU THR SEQRES 7 D 80 LEU LYS HET HEC A1082 43 HET HEC B1082 43 HET HEC C1082 43 HET HEC D1082 43 HETNAM HEC HEME C FORMUL 5 HEC 4(C34 H34 FE N4 O4) FORMUL 9 HOH *160(H2 O) HELIX 1 1 ASP A 1 ASN A 8 1 8 HELIX 2 2 ALA A 24 TYR A 32 1 9 HELIX 3 3 ASP A 37 GLY A 49 1 13 HELIX 4 4 SER A 66 LEU A 80 1 15 HELIX 5 5 ASP B 1 ASN B 8 1 8 HELIX 6 6 ASN B 9 HIS B 14 1 6 HELIX 7 7 ALA B 24 ALA B 33 1 10 HELIX 8 8 ASP B 37 GLY B 49 1 13 HELIX 9 9 SER B 66 LEU B 80 1 15 HELIX 10 10 ASP C 1 ASN C 8 1 8 HELIX 11 11 ASN C 9 CYS C 13 5 5 HELIX 12 12 ALA C 24 TYR C 32 1 9 HELIX 13 13 ASP C 37 GLY C 49 1 13 HELIX 14 14 SER C 66 LEU C 80 1 15 HELIX 15 15 ASP D 1 ASN D 8 1 8 HELIX 16 16 ASN D 9 HIS D 14 1 6 HELIX 17 17 ALA D 24 TYR D 32 1 9 HELIX 18 18 ASP D 37 GLY D 49 1 13 HELIX 19 19 SER D 66 THR D 79 1 14 LINK SG CYS A 10 CAB HEC A1082 1555 1555 1.73 LINK SG CYS A 13 CAC HEC A1082 1555 1555 1.92 LINK SG CYS B 10 CAB HEC B1082 1555 1555 1.70 LINK SG CYS B 13 CAC HEC B1082 1555 1555 2.07 LINK SG CYS C 10 CAB HEC C1082 1555 1555 1.69 LINK SG CYS C 13 CAC HEC C1082 1555 1555 1.91 LINK SG CYS D 10 CAB HEC D1082 1555 1555 1.89 LINK SG CYS D 13 CAC HEC D1082 1555 1555 1.81 LINK NE2 HIS A 14 FE HEC A1082 1555 1555 2.00 LINK SD MET A 59 FE HEC A1082 1555 1555 2.24 LINK NE2 HIS B 14 FE HEC B1082 1555 1555 2.13 LINK SD MET B 59 FE HEC B1082 1555 1555 2.48 LINK NE2 HIS C 14 FE HEC C1082 1555 1555 1.94 LINK SD MET C 59 FE HEC C1082 1555 1555 2.21 LINK NE2 HIS D 14 FE HEC D1082 1555 1555 2.02 LINK SD MET D 59 FE HEC D1082 1555 1555 2.26 SITE 1 AC1 23 ASN A 9 CYS A 10 CYS A 13 HIS A 14 SITE 2 AC1 23 GLY A 22 PRO A 23 ILE A 28 TYR A 32 SITE 3 AC1 23 TYR A 41 LYS A 45 ILE A 46 SER A 50 SITE 4 AC1 23 SER A 51 GLY A 52 VAL A 53 TRP A 54 SITE 5 AC1 23 GLY A 55 ILE A 57 PRO A 58 MET A 59 SITE 6 AC1 23 VAL A 63 HOH A2042 HEC C1082 SITE 1 AC2 22 ASN B 9 CYS B 10 CYS B 13 HIS B 14 SITE 2 AC2 22 GLY B 22 PRO B 23 ILE B 28 TYR B 32 SITE 3 AC2 22 TYR B 41 LYS B 45 ILE B 46 SER B 50 SITE 4 AC2 22 SER B 51 GLY B 52 VAL B 53 TRP B 54 SITE 5 AC2 22 GLY B 55 ILE B 57 PRO B 58 MET B 59 SITE 6 AC2 22 VAL B 63 HOH B2032 SITE 1 AC3 24 HEC A1082 ASN C 8 ASN C 9 CYS C 10 SITE 2 AC3 24 CYS C 13 HIS C 14 VAL C 21 GLY C 22 SITE 3 AC3 24 PRO C 23 ILE C 28 TYR C 32 TYR C 41 SITE 4 AC3 24 LEU C 42 LYS C 45 SER C 50 SER C 51 SITE 5 AC3 24 GLY C 52 VAL C 53 TRP C 54 GLY C 55 SITE 6 AC3 24 ILE C 57 MET C 59 VAL C 63 HOH C2018 SITE 1 AC4 21 ASN D 9 CYS D 10 CYS D 13 HIS D 14 SITE 2 AC4 21 GLY D 22 PRO D 23 TYR D 32 TYR D 41 SITE 3 AC4 21 LYS D 45 ILE D 46 SER D 50 SER D 51 SITE 4 AC4 21 GLY D 52 VAL D 53 TRP D 54 GLY D 55 SITE 5 AC4 21 ILE D 57 PRO D 58 MET D 59 VAL D 63 SITE 6 AC4 21 HOH D2020 CRYST1 138.520 81.240 42.280 90.00 105.17 90.00 C 1 2 1 16 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 0.007219 0.000000 0.001957 0.00000 SCALE2 0.000000 0.012309 0.000000 0.00000 SCALE3 0.000000 0.000000 0.024506 0.00000