HEADER ELECTRON TRANSPORT 14-JAN-15 3X35 TITLE CRYSTAL STRUCTURE OF THE REDUCED FORM OF THE SOLUBILIZED DOMAIN OF TITLE 2 PORCINE CYTOCHROME B5 IN FORM 2 CRYSTAL COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYTOCHROME B5; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: N-TERMINAL DOMAIN, UNP RESIDUES 1-94; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SUS SCROFA; SOURCE 3 ORGANISM_COMMON: PIG; SOURCE 4 ORGANISM_TAXID: 9823; SOURCE 5 GENE: CYB5A, CYB5; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PCPB5 KEYWDS HEME, ELECTRON TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR Y.HIRANO,S.KIMURA,T.TAMADA REVDAT 4 08-NOV-23 3X35 1 REMARK LINK REVDAT 3 25-DEC-19 3X35 1 JRNL REVDAT 2 22-NOV-17 3X35 1 REMARK REVDAT 1 15-JUL-15 3X35 0 JRNL AUTH Y.HIRANO,S.KIMURA,T.TAMADA JRNL TITL HIGH-RESOLUTION CRYSTAL STRUCTURES OF THE SOLUBILIZED DOMAIN JRNL TITL 2 OF PORCINE CYTOCHROME B5. JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 71 1572 2015 JRNL REFN ESSN 1399-0047 JRNL PMID 26143928 JRNL DOI 10.1107/S1399004715009438 REMARK 2 REMARK 2 RESOLUTION. 0.95 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELXL-97 REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 0.95 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : NULL REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : 0.139 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.139 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.182 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 2846 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 60296 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : NULL REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE (F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 705 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 47 REMARK 3 SOLVENT ATOMS : 200 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : NULL REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : NULL REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : NULL REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : NULL REMARK 3 NUMBER OF RESTRAINTS : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.015 REMARK 3 ANGLE DISTANCES (A) : 0.039 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : NULL REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.353 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : NULL REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : NULL REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.024 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : NULL REMARK 3 SIMILAR ADP COMPONENTS (A**2) : NULL REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: NULL REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH & HUBER REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3X35 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 27-JAN-15. REMARK 100 THE DEPOSITION ID IS D_1000097119. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-NOV-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : BL-5A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.90 REMARK 200 MONOCHROMATOR : SI 111 REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 58020 REMARK 200 RESOLUTION RANGE HIGH (A) : 0.950 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.8 REMARK 200 DATA REDUNDANCY : 7.300 REMARK 200 R MERGE (I) : 0.08400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 54.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 0.95 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 0.97 REMARK 200 COMPLETENESS FOR SHELL (%) : 87.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.30 REMARK 200 R MERGE FOR SHELL (I) : 0.43900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 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 1CYO REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.56 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.22 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 15% PEG 400, 3% PEG 3350, 0.1M SODIUM REMARK 280 ACETATE, PH 5.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 16.86000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 27.64950 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 25.63300 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 27.64950 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 16.86000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 25.63300 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 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 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 ALA A 2 REMARK 465 GLU A 3 REMARK 465 GLN A 4 REMARK 465 SER A 5 REMARK 465 ASP A 6 REMARK 465 LYS A 7 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 GLU A 43 C HIS A 44 N 0.183 REMARK 500 HIS A 44 CG HIS A 44 CD2 0.059 REMARK 500 GLY A 82 N GLY A 82 CA -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 LYS A 10 CA - C - N ANGL. DEV. = 15.5 DEGREES REMARK 500 LYS A 10 O - C - N ANGL. DEV. = -14.6 DEGREES REMARK 500 GLU A 16 OE1 - CD - OE2 ANGL. DEV. = -8.2 DEGREES REMARK 500 LYS A 19 CD - CE - NZ ANGL. DEV. = 18.5 DEGREES REMARK 500 ASP A 36 CB - CG - OD2 ANGL. DEV. = -6.0 DEGREES REMARK 500 ARG A 52 CD - NE - CZ ANGL. DEV. = -8.5 DEGREES REMARK 500 ARG A 52 NE - CZ - NH2 ANGL. DEV. = 4.0 DEGREES REMARK 500 PHE A 79 CB - CG - CD1 ANGL. DEV. = -4.5 DEGREES 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 HEM A 101 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 44 NE2 REMARK 620 2 HEM A 101 NA 92.0 REMARK 620 3 HEM A 101 NB 89.8 89.9 REMARK 620 4 HEM A 101 NC 89.6 178.4 90.5 REMARK 620 5 HEM A 101 ND 88.8 89.9 178.6 89.7 REMARK 620 6 HIS A 68 NE2 177.7 90.3 90.0 88.2 91.4 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 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A 102 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3X32 RELATED DB: PDB REMARK 900 THE SAME PROTEIN OF THE OXIDIZED FORM IN FORM 1 CRYSTAL. REMARK 900 RELATED ID: 3X33 RELATED DB: PDB REMARK 900 THE SAME PROTEIN OF THE OXIDIZED FORM IN FORM 2 CRYSTAL. REMARK 900 RELATED ID: 3X34 RELATED DB: PDB REMARK 900 THE SAME PROTEIN OF THE REDUCED FORM IN FORM 1 CRYSTAL. DBREF 3X35 A 1 94 UNP P00172 CYB5_PIG 1 94 SEQRES 1 A 94 MET ALA GLU GLN SER ASP LYS ALA VAL LYS TYR TYR THR SEQRES 2 A 94 LEU GLU GLU ILE GLN LYS HIS ASN ASN SER LYS SER THR SEQRES 3 A 94 TRP LEU ILE LEU HIS HIS LYS VAL TYR ASP LEU THR LYS SEQRES 4 A 94 PHE LEU GLU GLU HIS PRO GLY GLY GLU GLU VAL LEU ARG SEQRES 5 A 94 GLU GLN ALA GLY GLY ASP ALA THR GLU ASN PHE GLU ASP SEQRES 6 A 94 VAL GLY HIS SER THR ASP ALA ARG GLU LEU SER LYS THR SEQRES 7 A 94 PHE ILE ILE GLY GLU LEU HIS PRO ASP ASP ARG SER LYS SEQRES 8 A 94 ILE ALA LYS HET HEM A 101 45 HET ACT A 102 4 HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETNAM ACT ACETATE ION HETSYN HEM HEME FORMUL 2 HEM C34 H32 FE N4 O4 FORMUL 3 ACT C2 H3 O2 1- FORMUL 4 HOH *200(H2 O) HELIX 1 1 THR A 13 LYS A 19 1 7 HELIX 2 2 LYS A 39 GLU A 43 5 5 HELIX 3 3 GLU A 48 GLU A 53 1 6 HELIX 4 4 ALA A 59 GLY A 67 1 9 HELIX 5 5 SER A 69 LYS A 77 1 9 HELIX 6 6 PRO A 86 ILE A 92 5 7 SHEET 1 A 5 TYR A 11 TYR A 12 0 SHEET 2 A 5 ILE A 80 LEU A 84 1 O GLU A 83 N TYR A 12 SHEET 3 A 5 LYS A 33 ASP A 36 -1 N VAL A 34 O ILE A 81 SHEET 4 A 5 SER A 25 LEU A 30 -1 N LEU A 28 O TYR A 35 SHEET 5 A 5 ASN A 21 ASN A 22 -1 N ASN A 22 O SER A 25 LINK NE2 HIS A 44 FE HEM A 101 1555 1555 1.98 LINK NE2 HIS A 68 FE HEM A 101 1555 1555 1.97 SITE 1 AC1 21 HIS A 32 LEU A 37 PHE A 40 HIS A 44 SITE 2 AC1 21 PRO A 45 GLY A 46 VAL A 50 LEU A 51 SITE 3 AC1 21 GLN A 54 ASN A 62 PHE A 63 VAL A 66 SITE 4 AC1 21 HIS A 68 SER A 69 ALA A 72 SER A 76 SITE 5 AC1 21 ARG A 89 LYS A 94 HOH A 221 HOH A 288 SITE 6 AC1 21 HOH A 305 SITE 1 AC2 6 LYS A 24 SER A 25 TRP A 27 ASP A 36 SITE 2 AC2 6 THR A 38 LYS A 39 CRYST1 33.720 51.266 55.299 90.00 90.00 90.00 P 21 21 21 4 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.029656 0.000000 0.000000 0.00000 SCALE2 0.000000 0.019506 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018084 0.00000