HEADER PHOTOSYNTHESIS 27-FEB-18 5ZE8 TITLE CRYSTAL STRUCTURE OF A PENTA-HEME CYTOCHROME C552 FROM TITLE 2 THERMOCHROMATIUM TEPIDUM COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYTOCHROME C552; COMPND 3 CHAIN: A SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMOCHROMATIUM TEPIDUM; SOURCE 3 ORGANISM_TAXID: 1050 KEYWDS CYTOCHROME C, MULTIHEME, PURPLE SULFUR BACTERIA, PHOTOSYNTHESIS EXPDTA X-RAY DIFFRACTION AUTHOR L.-J.YU,J.-H.CHEN,J.-R.SHEN REVDAT 4 02-OCT-19 5ZE8 1 COMPND REMARK HET HETNAM REVDAT 4 2 1 HETSYN FORMUL LINK SITE REVDAT 4 3 1 ATOM REVDAT 3 20-FEB-19 5ZE8 1 JRNL REVDAT 2 16-MAY-18 5ZE8 1 JRNL REVDAT 1 25-APR-18 5ZE8 0 JRNL AUTH J.H.CHEN,L.J.YU,A.BOUSSAC,Z.Y.WANG-OTOMO,T.KUANG,J.R.SHEN JRNL TITL PROPERTIES AND STRUCTURE OF A LOW-POTENTIAL, PENTA-HEME JRNL TITL 2 CYTOCHROME C552FROM A THERMOPHILIC PURPLE SULFUR JRNL TITL 3 PHOTOSYNTHETIC BACTERIUM THERMOCHROMATIUM TEPIDUM. JRNL REF PHOTOSYN. RES. V. 139 281 2019 JRNL REFN ISSN 1573-5079 JRNL PMID 29691716 JRNL DOI 10.1007/S11120-018-0507-Y REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0189 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 68.28 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 45846 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) : 0.160 REMARK 3 R VALUE (WORKING SET) : 0.158 REMARK 3 FREE R VALUE : 0.191 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2437 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) : 1.60 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.64 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3382 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.52 REMARK 3 BIN R VALUE (WORKING SET) : 0.2250 REMARK 3 BIN FREE R VALUE SET COUNT : 171 REMARK 3 BIN FREE R VALUE : 0.2420 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2975 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 226 REMARK 3 SOLVENT ATOMS : 351 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.42 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.00000 REMARK 3 B22 (A**2) : 0.00000 REMARK 3 B33 (A**2) : 0.00000 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): 0.086 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.087 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.055 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.536 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.965 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.950 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3340 ; 0.023 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 2949 ; 0.003 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4585 ; 2.261 ; 2.060 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6834 ; 1.292 ; 3.003 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 385 ; 6.538 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 138 ;33.059 ;24.348 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 494 ;14.806 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 17 ;25.626 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 458 ; 0.165 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3757 ; 0.018 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 689 ; 0.018 ; 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL 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 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 : NULL 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 U VALUES : REFINED INDIVIDUALLY REMARK 4 REMARK 4 5ZE8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 07-MAR-18. REMARK 100 THE DEPOSITION ID IS D_1300006907. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-DEC-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL41XU REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 48283 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 68.280 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 12.90 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 25.0200 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.66 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.7 REMARK 200 DATA REDUNDANCY IN SHELL : 10.70 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 5.160 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SHELXDE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 36.05 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.92 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 3350, CALCIUM CHLORIDE, AMMONIUM REMARK 280 CHLORIDE, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K 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 72.35000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 19.55000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 72.35000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 19.55000 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 MET A 1 REMARK 465 THR A 2 REMARK 465 ARG A 3 REMARK 465 LEU A 4 REMARK 465 ARG A 5 REMARK 465 SER A 6 REMARK 465 LEU A 7 REMARK 465 TYR A 8 REMARK 465 ALA A 9 REMARK 465 CYS A 10 REMARK 465 MET A 11 REMARK 465 THR A 12 REMARK 465 ASN A 13 REMARK 465 GLY A 14 REMARK 465 TRP A 15 REMARK 465 PRO A 16 REMARK 465 VAL A 17 REMARK 465 LEU A 18 REMARK 465 LEU A 19 REMARK 465 ALA A 20 REMARK 465 LEU A 21 REMARK 465 ILE A 22 REMARK 465 LEU A 23 REMARK 465 GLN A 24 REMARK 465 ALA A 25 REMARK 465 PRO A 26 REMARK 465 ALA A 27 REMARK 465 ALA A 28 REMARK 465 GLN A 29 REMARK 465 ALA A 30 REMARK 465 GLU A 31 REMARK 465 PRO A 32 REMARK 465 GLY A 33 REMARK 465 ALA A 34 REMARK 465 ARG A 175 REMARK 465 SER A 176 REMARK 465 ASP A 177 REMARK 465 ASP A 178 REMARK 465 LEU A 179 REMARK 465 PHE A 180 REMARK 465 GLY A 181 REMARK 465 GLY A 182 REMARK 465 ALA A 183 REMARK 465 VAL A 184 REMARK 465 ASP A 185 REMARK 465 ALA A 186 REMARK 465 VAL A 187 REMARK 465 PRO A 188 REMARK 465 ASP A 189 REMARK 465 GLN A 190 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 OE2 GLU A 35 O HOH A 601 1.98 REMARK 500 OD1 ASP A 341 O HOH A 602 2.01 REMARK 500 O3 GOL A 507 O HOH A 603 2.07 REMARK 500 O HOH A 604 O HOH A 662 2.08 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 TYR A 101 CZ TYR A 101 OH 0.102 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 39 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES REMARK 500 ARG A 54 NE - CZ - NH1 ANGL. DEV. = 6.4 DEGREES REMARK 500 ARG A 54 NE - CZ - NH2 ANGL. DEV. = -5.0 DEGREES REMARK 500 ARG A 109 NE - CZ - NH2 ANGL. DEV. = -3.6 DEGREES REMARK 500 MET A 226 CG - SD - CE ANGL. DEV. = -11.8 DEGREES REMARK 500 ASP A 233 CB - CG - OD1 ANGL. DEV. = 5.4 DEGREES REMARK 500 ASP A 269 CB - CG - OD1 ANGL. DEV. = 6.1 DEGREES REMARK 500 ASP A 288 CB - CG - OD2 ANGL. DEV. = -6.2 DEGREES REMARK 500 ARG A 384 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 ARG A 384 NE - CZ - NH2 ANGL. DEV. = -4.6 DEGREES REMARK 500 ARG A 399 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 ARG A 399 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 VAL A 80 -65.19 -128.44 REMARK 500 ASN A 215 67.87 -154.50 REMARK 500 GLN A 242 40.19 -153.91 REMARK 500 LYS A 295 -123.01 72.36 REMARK 500 ASP A 341 -121.55 -111.82 REMARK 500 ASP A 347 75.05 -156.80 REMARK 500 HIS A 381 26.93 47.95 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 A 501 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 49 NE2 REMARK 620 2 HEC A 501 NA 88.6 REMARK 620 3 HEC A 501 NB 89.0 89.3 REMARK 620 4 HEC A 501 NC 91.2 179.4 90.2 REMARK 620 5 HEC A 501 ND 88.2 90.3 177.3 90.3 REMARK 620 6 HIS A 195 NE2 179.0 90.5 90.6 89.8 92.2 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HEC A 504 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 61 NE2 REMARK 620 2 HEC A 504 NA 90.0 REMARK 620 3 HEC A 504 NB 92.5 89.6 REMARK 620 4 HEC A 504 NC 90.8 179.0 90.9 REMARK 620 5 HEC A 504 ND 90.6 89.1 176.7 90.3 REMARK 620 6 HIS A 229 NE2 178.0 88.2 86.5 90.9 90.4 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HEC A 502 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 103 NE2 REMARK 620 2 HEC A 502 NA 93.9 REMARK 620 3 HEC A 502 NB 91.7 86.5 REMARK 620 4 HEC A 502 NC 91.7 174.2 91.8 REMARK 620 5 HEC A 502 ND 88.1 91.1 177.6 90.6 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HEC A 503 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 131 NE2 REMARK 620 2 HEC A 503 NA 89.4 REMARK 620 3 HEC A 503 NB 90.0 91.8 REMARK 620 4 HEC A 503 NC 90.9 179.5 87.8 REMARK 620 5 HEC A 503 ND 89.7 88.3 179.7 92.1 REMARK 620 6 HIS A 270 NE2 178.4 89.2 89.2 90.5 91.1 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HEC A 505 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 260 NE2 REMARK 620 2 HEC A 505 NA 88.2 REMARK 620 3 HEC A 505 NB 90.4 89.5 REMARK 620 4 HEC A 505 NC 89.0 176.4 88.3 REMARK 620 5 HEC A 505 ND 87.9 92.2 177.5 89.9 REMARK 620 6 HIS A 310 NE2 177.3 89.3 90.6 93.6 91.2 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 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue HEC A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue HEC A 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue HEC A 504 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue HEC A 505 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 506 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 507 DBREF 5ZE8 A 1 435 PDB 5ZE8 5ZE8 1 435 SEQRES 1 A 435 MET THR ARG LEU ARG SER LEU TYR ALA CYS MET THR ASN SEQRES 2 A 435 GLY TRP PRO VAL LEU LEU ALA LEU ILE LEU GLN ALA PRO SEQRES 3 A 435 ALA ALA GLN ALA GLU PRO GLY ALA GLU PRO ILE HIS ARG SEQRES 4 A 435 VAL SER SER GLU LEU CYS ALA ASN CYS HIS GLU ASP ILE SEQRES 5 A 435 TYR ARG GLN TRP LYS GLY SER MET HIS ALA LYS SER THR SEQRES 6 A 435 ALA LEU SER ASP PRO ILE HIS GLY LEU PHE TYR GLN GLN SEQRES 7 A 435 GLU VAL GLY ASP PRO THR ALA GLU GLY MET VAL HIS LYS SEQRES 8 A 435 LYS SER GLY LYS PHE PRO LEU CYS LEU TYR CYS HIS ALA SEQRES 9 A 435 PRO ASN ALA ALA ARG ASP GLN THR THR LYS LEU ASP ALA SEQRES 10 A 435 HIS PRO ALA TYR THR GLU GLY VAL ASN CYS VAL ALA CYS SEQRES 11 A 435 HIS THR LEU LYS THR TYR ASN GLY ILE GLN ASP ALA GLU SEQRES 12 A 435 GLY LYS LEU ARG TYR GLY ILE LYS ALA TYR ASP LEU SER SEQRES 13 A 435 ASP ARG LEU GLN ALA PRO ILE GLY PHE PRO ARG GLU LEU SEQRES 14 A 435 GLU ARG LEU LYS ALA ARG SER ASP ASP LEU PHE GLY GLY SEQRES 15 A 435 ALA VAL ASP ALA VAL PRO ASP GLN LYS PRO ASN PRO HIS SEQRES 16 A 435 LEU GLY GLU PRO VAL GLU LEU ASP GLY LYS THR ILE PRO SEQRES 17 A 435 ALA LEU THR MET GLU ALA ASN PRO ARG GLN LEU ARG THR SEQRES 18 A 435 SER ASP ALA CYS MET GLY CYS HIS ASP GLN ARG ASP ASN SEQRES 19 A 435 PRO GLN GLY VAL PRO LEU CYS GLN THR GLY LYS GLU PHE SEQRES 20 A 435 ILE ALA GLY GLY SER GLN VAL ALA CYS GLN THR CYS HIS SEQRES 21 A 435 MET PRO VAL ALA GLY GLY PHE ALA ASP HIS SER MET GLY SEQRES 22 A 435 GLY GLY HIS HIS GLU ALA MET LEU LYS ARG SER ILE VAL SEQRES 23 A 435 PHE ASP LEU THR THR LYS ALA ASP LYS GLU LYS ILE ALA SEQRES 24 A 435 ALA GLN VAL TRP ILE ARG ASN LEU GLN PRO HIS ALA MET SEQRES 25 A 435 PRO THR GLY ALA PRO PHE ARG ASN LEU TYR LEU LYS LEU SEQRES 26 A 435 THR ALA TYR ASP ALA SER GLY GLU VAL LEU TRP GLN ASN SEQRES 27 A 435 ALA ALA ASP HIS PRO SER LYS ASP ASP PRO ARG ALA TYR SEQRES 28 A 435 PHE ALA TYR GLY LEU ALA ASP ASP GLN GLY ASN PRO ALA SEQRES 29 A 435 PRO PRO PRO THR ALA THR LYS PRO GLY ASP ASP THR ARG SEQRES 30 A 435 LEU GLN PRO HIS GLU THR ARG GLU LEU ASN TYR GLU ILE SEQRES 31 A 435 PRO ALA LYS GLY VAL ALA LEU VAL ARG GLY GLU LEU TYR SEQRES 32 A 435 TYR ASN LEU LEU TRP PRO SER LEU VAL GLU LYS PHE THR SEQRES 33 A 435 GLN LEU PRO ALA GLU LEU THR ALA PRO VAL LEU ILE ALA SEQRES 34 A 435 VAL SER GLU LYS PRO ILE HET HEC A 501 43 HET HEC A 502 43 HET HEC A 503 43 HET HEC A 504 43 HET HEC A 505 43 HET SO4 A 506 5 HET GOL A 507 6 HETNAM HEC HEME C HETNAM SO4 SULFATE ION HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 HEC 5(C34 H34 FE N4 O4) FORMUL 7 SO4 O4 S 2- FORMUL 8 GOL C3 H8 O3 FORMUL 9 HOH *351(H2 O) HELIX 1 AA1 PRO A 36 VAL A 40 5 5 HELIX 2 AA2 SER A 41 ASN A 47 1 7 HELIX 3 AA3 HIS A 49 GLY A 58 1 10 HELIX 4 AA4 ASP A 69 VAL A 80 1 12 HELIX 5 AA5 CYS A 99 ALA A 104 1 6 HELIX 6 AA6 ALA A 104 ASP A 110 1 7 HELIX 7 AA7 HIS A 118 GLU A 123 1 6 HELIX 8 AA8 ASN A 126 THR A 132 1 7 HELIX 9 AA9 TYR A 148 LYS A 151 5 4 HELIX 10 AB1 ARG A 167 ALA A 174 1 8 HELIX 11 AB2 ASN A 215 THR A 221 1 7 HELIX 12 AB3 SER A 222 ALA A 224 5 3 HELIX 13 AB4 CYS A 225 ASP A 230 1 6 HELIX 14 AB5 GLN A 242 GLY A 251 1 10 HELIX 15 AB6 ALA A 255 MET A 261 1 7 HELIX 16 AB7 HIS A 277 SER A 284 1 8 HELIX 17 AB8 HIS A 342 ASP A 347 1 6 HELIX 18 AB9 TRP A 408 PHE A 415 1 8 HELIX 19 AC1 PRO A 419 ALA A 424 1 6 SHEET 1 AA1 2 LEU A 133 TYR A 136 0 SHEET 2 AA1 2 TYR A 153 LEU A 155 -1 O ASP A 154 N LYS A 134 SHEET 1 AA2 2 LEU A 159 ALA A 161 0 SHEET 2 AA2 2 MET A 212 ALA A 214 1 O GLU A 213 N LEU A 159 SHEET 1 AA3 2 VAL A 200 LEU A 202 0 SHEET 2 AA3 2 LYS A 205 ILE A 207 -1 O ILE A 207 N VAL A 200 SHEET 1 AA4 2 ARG A 232 ASP A 233 0 SHEET 2 AA4 2 PRO A 239 CYS A 241 -1 O LEU A 240 N ARG A 232 SHEET 1 AA5 2 VAL A 263 ALA A 264 0 SHEET 2 AA5 2 PHE A 267 ALA A 268 -1 O PHE A 267 N ALA A 264 SHEET 1 AA6 3 ILE A 285 ASP A 294 0 SHEET 2 AA6 3 LYS A 297A ASN A 306 -1 O TRP A 303 N ASP A 288 SHEET 3 AA6 3 THR A 383 PRO A 391 -1 O LEU A 386 N VAL A 302 SHEET 1 AA7 4 VAL A 334 GLN A 337 0 SHEET 2 AA7 4 ASN A 320 TYR A 328 -1 N ALA A 327 O LEU A 335 SHEET 3 AA7 4 TYR A 351 ALA A 357 -1 O PHE A 352 N LEU A 321 SHEET 4 AA7 4 LYS A 371 ASP A 375 -1 O LYS A 371 N ALA A 357 SHEET 1 AA8 4 VAL A 334 GLN A 337 0 SHEET 2 AA8 4 ASN A 320 TYR A 328 -1 N ALA A 327 O LEU A 335 SHEET 3 AA8 4 LEU A 397 ASN A 405 -1 O LEU A 397 N TYR A 328 SHEET 4 AA8 4 VAL A 426 PRO A 434 -1 O SER A 431 N GLY A 400 LINK SG CYS A 45 CAB HEC A 501 1555 1555 1.88 LINK SG CYS A 48 CAC HEC A 501 1555 1555 1.93 LINK NE2 HIS A 49 FE HEC A 501 1555 1555 2.08 LINK NE2 HIS A 61 FE HEC A 504 1555 1555 2.05 LINK SG CYS A 99 CAB HEC A 502 1555 1555 1.91 LINK SG CYS A 102 CAC HEC A 502 1555 1555 1.88 LINK NE2 HIS A 103 FE HEC A 502 1555 1555 2.13 LINK SG CYS A 127 CAB HEC A 503 1555 1555 1.85 LINK SG CYS A 130 CAC HEC A 503 1555 1555 1.93 LINK NE2 HIS A 131 FE HEC A 503 1555 1555 2.06 LINK NE2 HIS A 195 FE HEC A 501 1555 1555 2.09 LINK SG CYS A 225 CAB HEC A 504 1555 1555 1.90 LINK SG CYS A 228 CAC HEC A 504 1555 1555 1.91 LINK NE2 HIS A 229 FE HEC A 504 1555 1555 2.10 LINK SG CYS A 256 CAB HEC A 505 1555 1555 1.84 LINK SG CYS A 259 CAC HEC A 505 1555 1555 1.92 LINK NE2 HIS A 260 FE HEC A 505 1555 1555 2.08 LINK NE2 HIS A 270 FE HEC A 503 1555 1555 2.08 LINK NE2 HIS A 310 FE HEC A 505 1555 1555 2.05 CISPEP 1 MET A 312 PRO A 313 0 4.18 SITE 1 AC1 19 LEU A 44 CYS A 45 CYS A 48 HIS A 49 SITE 2 AC1 19 HIS A 131 ALA A 161 PRO A 162 ILE A 163 SITE 3 AC1 19 GLY A 164 PHE A 165 LYS A 191 PRO A 192 SITE 4 AC1 19 PRO A 194 HIS A 195 LEU A 210 MET A 212 SITE 5 AC1 19 HEC A 503 HOH A 681 HOH A 809 SITE 1 AC2 21 ASP A 69 ILE A 71 HIS A 72 PHE A 75 SITE 2 AC2 21 GLU A 79 LEU A 98 CYS A 99 CYS A 102 SITE 3 AC2 21 HIS A 103 TYR A 148 CYS A 228 HIS A 229 SITE 4 AC2 21 ARG A 232 HIS A 276 THR A 314 GLY A 315 SITE 5 AC2 21 ALA A 316 ARG A 319 HEC A 504 HEC A 505 SITE 6 AC2 21 HOH A 738 SITE 1 AC3 25 CYS A 45 HIS A 49 ILE A 52 TRP A 56 SITE 2 AC3 25 HIS A 61 VAL A 125 ASN A 126 CYS A 127 SITE 3 AC3 25 CYS A 130 HIS A 131 LEU A 219 ARG A 220 SITE 4 AC3 25 GLN A 257 MET A 261 PHE A 267 ALA A 268 SITE 5 AC3 25 HIS A 270 ARG A 283 HEC A 501 HEC A 504 SITE 6 AC3 25 HOH A 651 HOH A 669 HOH A 691 HOH A 809 SITE 7 AC3 25 HOH A 837 SITE 1 AC4 19 MET A 60 HIS A 61 SER A 64 ASP A 69 SITE 2 AC4 19 CYS A 102 ALA A 224 CYS A 225 CYS A 228 SITE 3 AC4 19 HIS A 229 HIS A 260 MET A 272 GLY A 274 SITE 4 AC4 19 GLY A 275 HIS A 276 HIS A 277 HEC A 502 SITE 5 AC4 19 HEC A 503 HOH A 735 HOH A 738 SITE 1 AC5 19 MET A 226 HIS A 229 VAL A 254 CYS A 256 SITE 2 AC5 19 THR A 258 CYS A 259 HIS A 260 GLY A 274 SITE 3 AC5 19 GLY A 275 LEU A 281 SER A 284 PRO A 309 SITE 4 AC5 19 HIS A 310 THR A 314 ARG A 319 TYR A 404 SITE 5 AC5 19 HEC A 502 HOH A 660 HOH A 738 SITE 1 AC6 4 ARG A 167 ASN A 193 HOH A 606 HOH A 633 SITE 1 AC7 4 LEU A 155 ILE A 435 HOH A 603 HOH A 607 CRYST1 144.700 39.100 68.650 90.00 109.31 90.00 C 1 2 1 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 0.006911 0.000000 0.002421 0.00000 SCALE2 0.000000 0.025575 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015434 0.00000