HEADER ELECTRON TRANSPORT 16-JUN-19 6K9J TITLE 0.98 A THREE-DIMENSIONAL STRUCTURE OF HORSE HEART CYTOCHROME C AT 110K COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYTOCHROME C; COMPND 3 CHAIN: A SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: EQUUS CABALLUS; SOURCE 3 ORGANISM_COMMON: HORSE; SOURCE 4 ORGANISM_TAXID: 9796; SOURCE 5 TISSUE: HEART KEYWDS ELECTRON TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR Y.SUGAWARA,S.ENDO REVDAT 3 06-NOV-24 6K9J 1 REMARK REVDAT 2 22-NOV-23 6K9J 1 REMARK REVDAT 1 17-JUN-20 6K9J 0 JRNL AUTH Y.SUGAWARA,S.ENDO JRNL TITL 0.98 A THREE-DIMENSIONAL STRUCTURE OF HORSE HEART CYTOCHROME JRNL TITL 2 C AT 110K JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 0.98 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELXL 2017/1 REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 0.98 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 3 CROSS-VALIDATION METHOD : FREE R-VALUE REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM SELECTION REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : NULL REMARK 3 FREE R VALUE (NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : NULL REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.120 REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : 0.119 REMARK 3 FREE R VALUE (F>4SIG(F)) : 0.141 REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : 5.090 REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : 2768 REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 54355 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 826 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 43 REMARK 3 SOLVENT ATOMS : 217 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) : NULL REMARK 3 ANGLE DISTANCES (A) : NULL REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : NULL REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : NULL REMARK 3 ZERO CHIRAL VOLUMES (A**3) : NULL REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : NULL REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : NULL 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 : NULL REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 6K9J COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 25-JUN-19. REMARK 100 THE DEPOSITION ID IS D_1300011471. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-MAY-16 REMARK 200 TEMPERATURE (KELVIN) : 110 REMARK 200 PH : 6.4 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU MICROMAX-007 HF REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54178 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RIGAKU SATURN 944+ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : CRYSALISPRO REMARK 200 DATA SCALING SOFTWARE : CRYSALISPRO REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 77173 REMARK 200 RESOLUTION RANGE HIGH (A) : 0.980 REMARK 200 RESOLUTION RANGE LOW (A) : 25.400 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 200 DATA REDUNDANCY : 5.200 REMARK 200 R MERGE (I) : 0.06200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 26.0200 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 0.98 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.01 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 2.80 REMARK 200 R MERGE FOR SHELL (I) : 0.30100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.430 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 1HRC REMARK 200 REMARK 200 REMARK: PLATE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 58.23 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.94 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.0-1.5M SODIUM CHLORIDE, 2.7-3.2M REMARK 280 AMMONIUM SULFATE, 0.1M SODIUM PHOSPHATE, PH 6.4, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y,X,Z+3/4 REMARK 290 4555 Y,-X,Z+1/4 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 21.24350 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 31.86525 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 10.62175 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 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 LYS A 27 -139.39 -121.79 REMARK 500 ASN A 70 87.30 -166.96 REMARK 500 PHE A 82 119.89 -160.06 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 515 DISTANCE = 6.17 ANGSTROMS REMARK 525 HOH A 516 DISTANCE = 6.97 ANGSTROMS REMARK 525 HOH A 517 DISTANCE = 7.08 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 HEC A 201 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 18 NE2 REMARK 620 2 HEC A 201 NA 88.5 REMARK 620 3 HEC A 201 NB 88.6 90.1 REMARK 620 4 HEC A 201 NC 92.3 176.5 93.3 REMARK 620 5 HEC A 201 ND 88.4 86.3 175.4 90.3 REMARK 620 6 MET A 80 SD 172.3 84.7 94.8 94.3 87.7 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 201 DBREF 6K9J A 1 104 UNP P00004 CYC_HORSE 2 105 SEQADV 6K9J ACE A 0 UNP P00004 ACETYLATION SEQRES 1 A 105 ACE GLY ASP VAL GLU LYS GLY LYS LYS ILE PHE VAL GLN SEQRES 2 A 105 LYS CYS ALA GLN CYS HIS THR VAL GLU LYS GLY GLY LYS SEQRES 3 A 105 HIS LYS THR GLY PRO ASN LEU HIS GLY LEU PHE GLY ARG SEQRES 4 A 105 LYS THR GLY GLN ALA PRO GLY PHE THR TYR THR ASP ALA SEQRES 5 A 105 ASN LYS ASN LYS GLY ILE THR TRP LYS GLU GLU THR LEU SEQRES 6 A 105 MET GLU TYR LEU GLU ASN PRO LYS LYS TYR ILE PRO GLY SEQRES 7 A 105 THR LYS MET ILE PHE ALA GLY ILE LYS LYS LYS THR GLU SEQRES 8 A 105 ARG GLU ASP LEU ILE ALA TYR LEU LYS LYS ALA THR ASN SEQRES 9 A 105 GLU HET ACE A 0 3 HET HEC A 201 43 HETNAM ACE ACETYL GROUP HETNAM HEC HEME C FORMUL 1 ACE C2 H4 O FORMUL 2 HEC C34 H34 FE N4 O4 FORMUL 3 HOH *217(H2 O) HELIX 1 AA1 ASP A 2 CYS A 14 1 13 HELIX 2 AA2 THR A 49 LYS A 55 1 7 HELIX 3 AA3 LYS A 60 ASN A 70 1 11 HELIX 4 AA4 ASN A 70 ILE A 75 1 6 HELIX 5 AA5 LYS A 87 THR A 102 1 16 LINK C ACE A 0 N GLY A 1 1555 1555 1.36 LINK SG CYS A 14 CAB HEC A 201 1555 1555 1.86 LINK SG CYS A 17 CAC HEC A 201 1555 1555 1.88 LINK NE2 HIS A 18 FE HEC A 201 1555 1555 1.98 LINK SD MET A 80 FE HEC A 201 1555 1555 2.29 SITE 1 AC1 22 LYS A 13 CYS A 14 CYS A 17 HIS A 18 SITE 2 AC1 22 THR A 28 GLY A 29 PRO A 30 THR A 40 SITE 3 AC1 22 GLY A 41 TYR A 48 THR A 49 ASN A 52 SITE 4 AC1 22 LYS A 55 TRP A 59 TYR A 67 THR A 78 SITE 5 AC1 22 LYS A 79 MET A 80 PHE A 82 HOH A 339 SITE 6 AC1 22 HOH A 409 HOH A 412 CRYST1 56.887 56.887 42.487 90.00 90.00 90.00 P 43 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 0.017579 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017579 0.000000 0.00000 SCALE3 0.000000 0.000000 0.023537 0.00000 HETATM 1 C ACE A 0 23.430 18.316 10.444 0.50 29.94 C ANISOU 1 C ACE A 0 3490 1392 5815 983 -1216 -231 C HETATM 2 O ACE A 0 23.629 18.376 11.698 0.50 29.86 O ANISOU 2 O ACE A 0 3541 1778 5352 -150 -453 -1317 O HETATM 3 CH3 ACE A 0 23.984 19.393 9.561 0.50 35.70 C ANISOU 3 CH3 ACE A 0 4551 1413 6792 713 -1120 -30 C