HEADER ELECTRON TRANSPORT 25-MAY-11 2YK3 TITLE CRITHIDIA FASCICULATA CYTOCHROME C COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYTOCHROME C; COMPND 3 CHAIN: A, B, C; COMPND 4 SYNONYM: CYTOCHROME C555 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CRITHIDIA FASCICULATA; SOURCE 3 ORGANISM_TAXID: 5656 KEYWDS ELECTRON TRANSPORT, INTERMEMBRANE SPACE, METAL-BINDING, THIOETHER KEYWDS 2 BOND, RESPIRATORY CHAIN, TRYPANOSOME, MITOCHONDRION EXPDTA X-RAY DIFFRACTION AUTHOR V.FULOP,K.A.SAM,S.J.FERGUSON,M.L.GINGER,J.W.A.ALLEN REVDAT 4 20-DEC-23 2YK3 1 REMARK REVDAT 3 25-SEP-19 2YK3 1 COMPND REMARK HET HETNAM REVDAT 3 2 1 HETSYN FORMUL LINK ATOM REVDAT 2 17-APR-13 2YK3 1 JRNL REMARK VERSN REVDAT 1 15-JUN-11 2YK3 0 SPRSDE 15-JUN-11 2YK3 2W9K JRNL AUTH V.FULOP,K.A.SAM,S.J.FERGUSON,M.L.GINGER,J.W.A.ALLEN JRNL TITL STRUCTURE OF A TRYPANOSOMATID MITOCHONDRIAL CYTOCHROME C JRNL TITL 2 WITH HEME ATTACHED VIA ONLY ONE THIOETHER BOND AND JRNL TITL 3 IMPLICATIONS FOR THE SUBSTRATE RECOGNITION REQUIREMENTS OF JRNL TITL 4 HEME LYASE. JRNL REF FEBS J. V. 276 2822 2009 JRNL REFN ISSN 1742-464X JRNL PMID 19459937 JRNL DOI 10.1111/J.1742-4658.2009.07005.X REMARK 2 REMARK 2 RESOLUTION. 1.55 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0109 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) : 1.55 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 55.81 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 97.1 REMARK 3 NUMBER OF REFLECTIONS : 57638 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) : 0.208 REMARK 3 R VALUE (WORKING SET) : 0.206 REMARK 3 FREE R VALUE : 0.241 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2411 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) : 1.55 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.59 REMARK 3 REFLECTION IN BIN (WORKING SET) : 4073 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 93.05 REMARK 3 BIN R VALUE (WORKING SET) : 0.3210 REMARK 3 BIN FREE R VALUE SET COUNT : 171 REMARK 3 BIN FREE R VALUE : 0.3370 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2469 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 164 REMARK 3 SOLVENT ATOMS : 563 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 21.56 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 24.66 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.87000 REMARK 3 B22 (A**2) : -0.26000 REMARK 3 B33 (A**2) : 0.33000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.71000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.088 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.090 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.061 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.822 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.948 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.930 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2719 ; 0.015 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3705 ; 2.190 ; 2.062 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 327 ; 6.402 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 102 ;32.839 ;23.824 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 393 ;12.738 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 15 ;17.444 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 354 ; 0.096 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2088 ; 0.012 ; 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): 1626 ; 0.843 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2568 ; 1.344 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1087 ; 2.306 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1137 ; 3.357 ; 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 : 6 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 5 A 71 REMARK 3 ORIGIN FOR THE GROUP (A): 15.2960 19.9950 7.6730 REMARK 3 T TENSOR REMARK 3 T11: 0.0923 T22: 0.0659 REMARK 3 T33: 0.0360 T12: 0.0254 REMARK 3 T13: -0.0436 T23: -0.0200 REMARK 3 L TENSOR REMARK 3 L11: 0.8923 L22: 1.9518 REMARK 3 L33: 1.0086 L12: 0.6813 REMARK 3 L13: 0.2416 L23: -0.0132 REMARK 3 S TENSOR REMARK 3 S11: -0.0043 S12: 0.0465 S13: -0.0513 REMARK 3 S21: -0.1987 S22: 0.0594 S23: -0.0428 REMARK 3 S31: 0.1529 S32: 0.1338 S33: -0.0552 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 72 A 114 REMARK 3 ORIGIN FOR THE GROUP (A): 12.0270 15.4420 12.9450 REMARK 3 T TENSOR REMARK 3 T11: 0.1376 T22: 0.0162 REMARK 3 T33: 0.0689 T12: 0.0036 REMARK 3 T13: -0.0786 T23: -0.0002 REMARK 3 L TENSOR REMARK 3 L11: 1.6774 L22: 2.1843 REMARK 3 L33: 1.4543 L12: 1.2970 REMARK 3 L13: 0.4322 L23: 0.8080 REMARK 3 S TENSOR REMARK 3 S11: 0.1297 S12: -0.0509 S13: -0.1339 REMARK 3 S21: 0.0940 S22: -0.0676 S23: -0.0850 REMARK 3 S31: 0.3011 S32: -0.0285 S33: -0.0621 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 5 B 71 REMARK 3 ORIGIN FOR THE GROUP (A): 0.4040 37.6060 22.4230 REMARK 3 T TENSOR REMARK 3 T11: 0.0356 T22: 0.0949 REMARK 3 T33: 0.0752 T12: -0.0200 REMARK 3 T13: -0.0204 T23: -0.0270 REMARK 3 L TENSOR REMARK 3 L11: 0.8989 L22: 1.6870 REMARK 3 L33: 0.9085 L12: -0.8556 REMARK 3 L13: -0.4166 L23: 0.4385 REMARK 3 S TENSOR REMARK 3 S11: -0.0259 S12: 0.0274 S13: -0.1509 REMARK 3 S21: 0.0682 S22: -0.1242 S23: 0.1969 REMARK 3 S31: 0.0643 S32: -0.1450 S33: 0.1501 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 72 B 114 REMARK 3 ORIGIN FOR THE GROUP (A): 0.7070 45.1720 24.1380 REMARK 3 T TENSOR REMARK 3 T11: 0.0371 T22: 0.0909 REMARK 3 T33: 0.0646 T12: 0.0158 REMARK 3 T13: -0.0428 T23: -0.0404 REMARK 3 L TENSOR REMARK 3 L11: 2.1337 L22: 1.2336 REMARK 3 L33: 0.7416 L12: -0.9074 REMARK 3 L13: -0.2061 L23: 0.2065 REMARK 3 S TENSOR REMARK 3 S11: -0.0385 S12: -0.0179 S13: 0.0724 REMARK 3 S21: 0.0237 S22: -0.0500 S23: 0.0539 REMARK 3 S31: -0.0294 S32: -0.0767 S33: 0.0885 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 5 C 71 REMARK 3 ORIGIN FOR THE GROUP (A): 18.7790 46.9620 4.1650 REMARK 3 T TENSOR REMARK 3 T11: 0.0548 T22: 0.0941 REMARK 3 T33: 0.1084 T12: -0.0199 REMARK 3 T13: -0.0548 T23: 0.0648 REMARK 3 L TENSOR REMARK 3 L11: 1.5968 L22: 0.5974 REMARK 3 L33: 2.1642 L12: -0.0827 REMARK 3 L13: 0.0364 L23: -0.2424 REMARK 3 S TENSOR REMARK 3 S11: -0.0954 S12: 0.2662 S13: 0.3261 REMARK 3 S21: 0.0361 S22: 0.0116 S23: 0.0536 REMARK 3 S31: -0.1874 S32: 0.0767 S33: 0.0839 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 72 C 114 REMARK 3 ORIGIN FOR THE GROUP (A): 24.6970 43.9850 0.2760 REMARK 3 T TENSOR REMARK 3 T11: 0.0321 T22: 0.2094 REMARK 3 T33: 0.0582 T12: -0.0393 REMARK 3 T13: -0.0394 T23: 0.0808 REMARK 3 L TENSOR REMARK 3 L11: 2.0457 L22: 0.7881 REMARK 3 L33: 3.1200 L12: -0.2933 REMARK 3 L13: 1.3277 L23: -0.6313 REMARK 3 S TENSOR REMARK 3 S11: -0.0969 S12: 0.5217 S13: 0.2042 REMARK 3 S21: -0.0115 S22: -0.0775 S23: -0.0516 REMARK 3 S31: -0.0452 S32: 0.4154 S33: 0.1744 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 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 2YK3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 25-MAY-11. REMARK 100 THE DEPOSITION ID IS D_1290048430. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-APR-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I02 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9511 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 60049 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.550 REMARK 200 RESOLUTION RANGE LOW (A) : 56.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.6 REMARK 200 DATA REDUNDANCY : 6.500 REMARK 200 R MERGE (I) : 0.12000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.55 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.61 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 6.60 REMARK 200 R MERGE FOR SHELL (I) : 0.69000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.000 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 1YCC REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.20 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2.45 M (NH4)2 SO4, 0.1 M HEPES (PH REMARK 280 6.5)., VAPOR DIFFUSION, HANGING DROP 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 42.96500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 55.44000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 42.96500 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 55.44000 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: HEXAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: HEXAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 16720 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 30070 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -343.4 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, 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 BIOMT1 2 -1.000000 0.000000 0.000000 45.79605 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 45.84464 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A2028 LIES ON A SPECIAL POSITION. 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 PRO A 2 REMARK 465 PRO A 3 REMARK 465 LYS A 4 REMARK 465 MET B 1 REMARK 465 PRO B 2 REMARK 465 PRO B 3 REMARK 465 LYS B 4 REMARK 465 MET C 1 REMARK 465 PRO C 2 REMARK 465 PRO C 3 REMARK 465 LYS C 4 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 ASN A 81 89.73 -159.46 REMARK 500 ASN B 81 92.21 -164.50 REMARK 500 ASN C 81 93.88 -162.91 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 A2049 DISTANCE = 6.28 ANGSTROMS REMARK 525 HOH A2097 DISTANCE = 6.19 ANGSTROMS REMARK 525 HOH A2113 DISTANCE = 5.93 ANGSTROMS REMARK 525 HOH B2026 DISTANCE = 7.17 ANGSTROMS REMARK 525 HOH B2056 DISTANCE = 6.25 ANGSTROMS REMARK 525 HOH C2005 DISTANCE = 6.09 ANGSTROMS REMARK 525 HOH C2029 DISTANCE = 5.97 ANGSTROMS REMARK 525 HOH C2064 DISTANCE = 6.00 ANGSTROMS REMARK 525 HOH C2079 DISTANCE = 6.67 ANGSTROMS REMARK 600 REMARK 600 HETEROGEN REMARK 600 REMARK 600 HEME (HEM): HEME ATTACHED VIA ONLY ONE THIOETHER BOND 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 A 200 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 29 NE2 REMARK 620 2 HEC A 200 NA 92.7 REMARK 620 3 HEC A 200 NB 88.4 89.0 REMARK 620 4 HEC A 200 NC 87.8 179.4 90.6 REMARK 620 5 HEC A 200 ND 91.2 90.6 179.4 89.8 REMARK 620 6 MET A 91 SD 173.0 82.7 96.8 96.9 83.6 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HEC B 200 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 29 NE2 REMARK 620 2 HEC B 200 NA 92.3 REMARK 620 3 HEC B 200 NB 87.9 91.4 REMARK 620 4 HEC B 200 NC 88.5 179.3 88.5 REMARK 620 5 HEC B 200 ND 92.4 89.4 179.1 90.7 REMARK 620 6 MET B 91 SD 174.4 83.5 95.7 95.8 84.0 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HEC C 200 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS C 29 NE2 REMARK 620 2 HEC C 200 NA 93.6 REMARK 620 3 HEC C 200 NB 86.5 90.2 REMARK 620 4 HEC C 200 NC 86.9 179.4 90.2 REMARK 620 5 HEC C 200 ND 93.6 89.2 179.5 90.3 REMARK 620 6 MET C 91 SD 176.1 84.4 96.8 95.1 83.1 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 HEM A 200 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1115 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1116 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1117 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HEM B 200 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 1115 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 1116 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HEM C 200 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 C 1115 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 C 1116 DBREF 2YK3 A 1 114 UNP P00078 CYC_CRIFA 1 114 DBREF 2YK3 B 1 114 UNP P00078 CYC_CRIFA 1 114 DBREF 2YK3 C 1 114 UNP P00078 CYC_CRIFA 1 114 SEQRES 1 A 114 MET PRO PRO LYS ALA ARG ALA PRO LEU PRO PRO GLY ASP SEQRES 2 A 114 ALA ALA ARG GLY GLU LYS LEU PHE LYS GLY ARG ALA ALA SEQRES 3 A 114 GLN CYS HIS THR ALA ASN GLN GLY GLY ALA ASN GLY VAL SEQRES 4 A 114 GLY PRO ASN LEU TYR GLY LEU VAL GLY ARG HIS SER GLY SEQRES 5 A 114 THR ILE GLU GLY TYR ALA TYR SER LYS ALA ASN ALA GLU SEQRES 6 A 114 SER GLY VAL VAL TRP THR PRO ASP VAL LEU ASP VAL TYR SEQRES 7 A 114 LEU GLU ASN PRO M3L LYS PHE MET PRO GLY THR LYS MET SEQRES 8 A 114 SER PHE ALA GLY MET LYS LYS PRO GLN GLU ARG ALA ASP SEQRES 9 A 114 VAL ILE ALA TYR LEU GLU THR LEU LYS GLY SEQRES 1 B 114 MET PRO PRO LYS ALA ARG ALA PRO LEU PRO PRO GLY ASP SEQRES 2 B 114 ALA ALA ARG GLY GLU LYS LEU PHE LYS GLY ARG ALA ALA SEQRES 3 B 114 GLN CYS HIS THR ALA ASN GLN GLY GLY ALA ASN GLY VAL SEQRES 4 B 114 GLY PRO ASN LEU TYR GLY LEU VAL GLY ARG HIS SER GLY SEQRES 5 B 114 THR ILE GLU GLY TYR ALA TYR SER LYS ALA ASN ALA GLU SEQRES 6 B 114 SER GLY VAL VAL TRP THR PRO ASP VAL LEU ASP VAL TYR SEQRES 7 B 114 LEU GLU ASN PRO M3L LYS PHE MET PRO GLY THR LYS MET SEQRES 8 B 114 SER PHE ALA GLY MET LYS LYS PRO GLN GLU ARG ALA ASP SEQRES 9 B 114 VAL ILE ALA TYR LEU GLU THR LEU LYS GLY SEQRES 1 C 114 MET PRO PRO LYS ALA ARG ALA PRO LEU PRO PRO GLY ASP SEQRES 2 C 114 ALA ALA ARG GLY GLU LYS LEU PHE LYS GLY ARG ALA ALA SEQRES 3 C 114 GLN CYS HIS THR ALA ASN GLN GLY GLY ALA ASN GLY VAL SEQRES 4 C 114 GLY PRO ASN LEU TYR GLY LEU VAL GLY ARG HIS SER GLY SEQRES 5 C 114 THR ILE GLU GLY TYR ALA TYR SER LYS ALA ASN ALA GLU SEQRES 6 C 114 SER GLY VAL VAL TRP THR PRO ASP VAL LEU ASP VAL TYR SEQRES 7 C 114 LEU GLU ASN PRO M3L LYS PHE MET PRO GLY THR LYS MET SEQRES 8 C 114 SER PHE ALA GLY MET LYS LYS PRO GLN GLU ARG ALA ASP SEQRES 9 C 114 VAL ILE ALA TYR LEU GLU THR LEU LYS GLY MODRES 2YK3 M3L A 83 LYS N-TRIMETHYLLYSINE MODRES 2YK3 M3L B 83 LYS N-TRIMETHYLLYSINE MODRES 2YK3 M3L C 83 LYS N-TRIMETHYLLYSINE HET M3L A 83 12 HET M3L B 83 12 HET M3L C 83 12 HET HEC A 200 43 HET SO4 A1115 5 HET SO4 A1116 5 HET SO4 A1117 5 HET HEC B 200 43 HET SO4 B1115 5 HET SO4 B1116 5 HET HEC C 200 43 HET SO4 C1115 5 HET SO4 C1116 5 HETNAM M3L N-TRIMETHYLLYSINE HETNAM HEC HEME C HETNAM SO4 SULFATE ION FORMUL 1 M3L 3(C9 H21 N2 O2 1+) FORMUL 4 HEC 3(C34 H34 FE N4 O4) FORMUL 5 SO4 7(O4 S 2-) FORMUL 14 HOH *563(H2 O) HELIX 1 1 ASP A 13 ALA A 25 1 13 HELIX 2 2 SER A 60 SER A 66 1 7 HELIX 3 3 THR A 71 ASN A 81 1 11 HELIX 4 4 ASN A 81 MET A 86 1 6 HELIX 5 5 LYS A 98 THR A 111 1 14 HELIX 6 6 ASP B 13 ALA B 25 1 13 HELIX 7 7 SER B 60 SER B 66 1 7 HELIX 8 8 THR B 71 ASN B 81 1 11 HELIX 9 9 ASN B 81 MET B 86 1 6 HELIX 10 10 LYS B 98 THR B 111 1 14 HELIX 11 11 ASP C 13 ALA C 25 1 13 HELIX 12 12 SER C 60 SER C 66 1 7 HELIX 13 13 THR C 71 ASN C 81 1 11 HELIX 14 14 ASN C 81 MET C 86 1 6 HELIX 15 15 LYS C 98 THR C 111 1 14 LINK SG CYS A 28 CAC HEC A 200 1555 1555 1.85 LINK C PRO A 82 N M3L A 83 1555 1555 1.33 LINK C M3L A 83 N LYS A 84 1555 1555 1.33 LINK SG CYS B 28 CAC HEC B 200 1555 1555 1.85 LINK C PRO B 82 N M3L B 83 1555 1555 1.32 LINK C M3L B 83 N LYS B 84 1555 1555 1.33 LINK SG CYS C 28 CAC HEC C 200 1555 1555 1.89 LINK C PRO C 82 N M3L C 83 1555 1555 1.34 LINK C M3L C 83 N LYS C 84 1555 1555 1.34 LINK NE2 HIS A 29 FE HEC A 200 1555 1555 2.02 LINK SD MET A 91 FE HEC A 200 1555 1555 2.29 LINK NE2 HIS B 29 FE HEC B 200 1555 1555 2.00 LINK SD MET B 91 FE HEC B 200 1555 1555 2.27 LINK NE2 HIS C 29 FE HEC C 200 1555 1555 2.00 LINK SD MET C 91 FE HEC C 200 1555 1555 2.27 SITE 1 AC1 24 ARG A 24 ALA A 25 GLN A 27 CYS A 28 SITE 2 AC1 24 HIS A 29 VAL A 39 LEU A 46 SER A 51 SITE 3 AC1 24 GLY A 52 ILE A 54 TYR A 57 TYR A 59 SITE 4 AC1 24 SER A 60 ASN A 63 TRP A 70 TYR A 78 SITE 5 AC1 24 LEU A 79 THR A 89 LYS A 90 MET A 91 SITE 6 AC1 24 SER A 92 HOH A2121 ASN B 37 GLY B 38 SITE 1 AC2 8 ARG A 24 GLY A 95 MET A 96 LYS A 97 SITE 2 AC2 8 HOH A2067 HOH A2178 HOH A2182 HOH A2197 SITE 1 AC3 3 ARG A 49 HOH A2122 HOH A2198 SITE 1 AC4 9 LYS A 90 HOH A2172 HOH A2199 HOH A2200 SITE 2 AC4 9 HOH A2201 HOH A2202 HOH A2203 LYS B 90 SITE 3 AC4 9 LYS C 90 SITE 1 AC5 23 ARG B 24 ALA B 25 GLN B 27 CYS B 28 SITE 2 AC5 23 HIS B 29 VAL B 39 LEU B 46 SER B 51 SITE 3 AC5 23 GLY B 52 ILE B 54 TYR B 57 TYR B 59 SITE 4 AC5 23 SER B 60 ASN B 63 TRP B 70 TYR B 78 SITE 5 AC5 23 LEU B 79 THR B 89 LYS B 90 MET B 91 SITE 6 AC5 23 SER B 92 HOH B2120 ASN C 37 SITE 1 AC6 9 ARG B 24 GLY B 95 MET B 96 LYS B 97 SITE 2 AC6 9 HOH B2173 HOH B2174 HOH B2177 HOH B2189 SITE 3 AC6 9 HOH B2190 SITE 1 AC7 3 ARG B 49 HOH B2121 HOH B2122 SITE 1 AC8 24 ASN A 37 ARG C 24 ALA C 25 GLN C 27 SITE 2 AC8 24 CYS C 28 HIS C 29 VAL C 39 LEU C 43 SITE 3 AC8 24 LEU C 46 SER C 51 GLY C 52 ILE C 54 SITE 4 AC8 24 TYR C 57 TYR C 59 SER C 60 ASN C 63 SITE 5 AC8 24 TRP C 70 TYR C 78 LEU C 79 THR C 89 SITE 6 AC8 24 LYS C 90 MET C 91 SER C 92 HOH C2096 SITE 1 AC9 7 ARG C 24 GLY C 95 LYS C 97 HOH C2050 SITE 2 AC9 7 HOH C2150 HOH C2157 HOH C2170 SITE 1 BC1 4 ARG C 49 HOH C2097 HOH C2103 HOH C2107 CRYST1 85.930 110.880 60.930 90.00 131.20 90.00 C 1 2 1 12 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 0.011637 0.000000 0.010188 0.00000 SCALE2 0.000000 0.009019 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021813 0.00000