HEADER OXIDOREDUCTASE 12-JUN-24 9C8L TITLE HIGH-RESOLUTION STRUCTURE OF CYTOCHROME C PEROXIDASE FROM YEAST AT TITLE 2 AMBIENT TEMPERATURE AND AMBIENT PRESSURE COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYTOCHROME C PEROXIDASE, MITOCHONDRIAL; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: CCP; COMPND 5 EC: 1.11.1.5; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE (STRAIN ATCC 204508 / SOURCE 3 S288C); SOURCE 4 ORGANISM_COMMON: BREWER'S YEAST; SOURCE 5 ORGANISM_TAXID: 559292; SOURCE 6 STRAIN: ATCC 204508 / S288C; SOURCE 7 GENE: CCP1, CCP, CPO, YKR066C; SOURCE 8 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS ELECTRON TRANSFER, HYDROGEN PEROXIDE, HIGH-PRESSURE, DIAMOND ANVIL KEYWDS 2 CELL, PEROXIDASE, CYTOCHROME, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR R.K.ZAWISTOWSKI,B.R.CRANE REVDAT 2 23-OCT-24 9C8L 1 JRNL REVDAT 1 16-OCT-24 9C8L 0 JRNL AUTH R.K.ZAWISTOWSKI,B.R.CRANE JRNL TITL DIFFERENTIAL RESPONSES IN THE CORE, ACTIVE SITE AND JRNL TITL 2 PERIPHERAL REGIONS OF CYTOCHROME C PEROXIDASE TO EXTREME JRNL TITL 3 PRESSURE AND TEMPERATURE. JRNL REF J.MOL.BIOL. V. 436 68799 2024 JRNL REFN ESSN 1089-8638 JRNL PMID 39332669 JRNL DOI 10.1016/J.JMB.2024.168799 REMARK 2 REMARK 2 RESOLUTION. 1.54 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.21_5207 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.54 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.92 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.1 REMARK 3 NUMBER OF REFLECTIONS : 50414 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.156 REMARK 3 R VALUE (WORKING SET) : 0.155 REMARK 3 FREE R VALUE : 0.180 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.970 REMARK 3 FREE R VALUE TEST SET COUNT : 2000 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 34.9200 - 3.7100 1.00 3747 154 0.1143 0.1364 REMARK 3 2 3.7100 - 2.9500 1.00 3605 150 0.1440 0.1729 REMARK 3 3 2.9500 - 2.5700 1.00 3536 145 0.1579 0.1556 REMARK 3 4 2.5700 - 2.3400 1.00 3520 147 0.1604 0.2030 REMARK 3 5 2.3400 - 2.1700 1.00 3494 144 0.1641 0.2213 REMARK 3 6 2.1700 - 2.0400 0.99 3507 145 0.1628 0.1932 REMARK 3 7 2.0400 - 1.9400 0.99 3459 142 0.1750 0.1971 REMARK 3 8 1.9400 - 1.8600 0.99 3434 143 0.1843 0.2055 REMARK 3 9 1.8600 - 1.7800 0.98 3448 141 0.1697 0.1919 REMARK 3 10 1.7800 - 1.7200 0.98 3399 141 0.1712 0.1858 REMARK 3 11 1.7200 - 1.6700 0.97 3385 140 0.1874 0.2201 REMARK 3 12 1.6700 - 1.6200 0.96 3341 138 0.2126 0.2269 REMARK 3 13 1.6200 - 1.5800 0.96 3319 137 0.2854 0.2803 REMARK 3 14 1.5800 - 1.5400 0.93 3220 133 0.3649 0.3808 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.194 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 17.382 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 21.81 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.00 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.011 2517 REMARK 3 ANGLE : 1.101 3428 REMARK 3 CHIRALITY : 0.062 338 REMARK 3 PLANARITY : 0.009 450 REMARK 3 DIHEDRAL : 16.020 912 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 9C8L COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-JUN-24. REMARK 100 THE DEPOSITION ID IS D_1000283027. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-AUG-22 REMARK 200 TEMPERATURE (KELVIN) : 293 REMARK 200 PH : 6.1-7.1 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS-II REMARK 200 BEAMLINE : 17-ID-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97933 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : HKL-2000 V722 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 50414 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.540 REMARK 200 RESOLUTION RANGE LOW (A) : 34.920 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.1 REMARK 200 DATA REDUNDANCY : 3.200 REMARK 200 R MERGE (I) : 0.09200 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 20.8100 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.54 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.57 REMARK 200 COMPLETENESS FOR SHELL (%) : 91.9 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.74700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 0.880 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX 1.21_5207 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: RED, LONG AND ROD-SHAPED REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.25 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.52 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10-25 % POLYETHYLENE GLYCOL 550 (MME) REMARK 280 AND 100 MM 2-(N-MORPHOLINO)ETHANESULFONIC ACID (PH 6.1-7.1), REMARK 280 VAPOR DIFFUSION, SITTING 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 22.57150 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 50.74650 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 37.19200 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 50.74650 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 22.57150 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 37.19200 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 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LEU A 4 CD1 REMARK 470 LYS A 12 NZ 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 ASP A 148 56.93 -97.46 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 301 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 175 NE2 REMARK 620 2 HEM A 301 NA 98.9 REMARK 620 3 HEM A 301 NB 96.0 89.2 REMARK 620 4 HEM A 301 NC 92.3 168.8 89.4 REMARK 620 5 HEM A 301 ND 95.5 89.9 168.5 89.3 REMARK 620 6 HOH A 521 O 172.4 74.1 81.3 94.7 87.4 REMARK 620 N 1 2 3 4 5 DBREF 9C8L A 1 294 UNP P00431 CCPR_YEAST 68 361 SEQADV 9C8L MET A -1 UNP P00431 INITIATING METHIONINE SEQADV 9C8L ILE A 0 UNP P00431 EXPRESSION TAG SEQADV 9C8L ILE A 53 UNP P00431 THR 120 VARIANT SEQADV 9C8L GLY A 152 UNP P00431 ASP 219 VARIANT SEQRES 1 A 296 MET ILE THR THR PRO LEU VAL HIS VAL ALA SER VAL GLU SEQRES 2 A 296 LYS GLY ARG SER TYR GLU ASP PHE GLN LYS VAL TYR ASN SEQRES 3 A 296 ALA ILE ALA LEU LYS LEU ARG GLU ASP ASP GLU TYR ASP SEQRES 4 A 296 ASN TYR ILE GLY TYR GLY PRO VAL LEU VAL ARG LEU ALA SEQRES 5 A 296 TRP HIS ILE SER GLY THR TRP ASP LYS HIS ASP ASN THR SEQRES 6 A 296 GLY GLY SER TYR GLY GLY THR TYR ARG PHE LYS LYS GLU SEQRES 7 A 296 PHE ASN ASP PRO SER ASN ALA GLY LEU GLN ASN GLY PHE SEQRES 8 A 296 LYS PHE LEU GLU PRO ILE HIS LYS GLU PHE PRO TRP ILE SEQRES 9 A 296 SER SER GLY ASP LEU PHE SER LEU GLY GLY VAL THR ALA SEQRES 10 A 296 VAL GLN GLU MET GLN GLY PRO LYS ILE PRO TRP ARG CYS SEQRES 11 A 296 GLY ARG VAL ASP THR PRO GLU ASP THR THR PRO ASP ASN SEQRES 12 A 296 GLY ARG LEU PRO ASP ALA ASP LYS ASP ALA GLY TYR VAL SEQRES 13 A 296 ARG THR PHE PHE GLN ARG LEU ASN MET ASN ASP ARG GLU SEQRES 14 A 296 VAL VAL ALA LEU MET GLY ALA HIS ALA LEU GLY LYS THR SEQRES 15 A 296 HIS LEU LYS ASN SER GLY TYR GLU GLY PRO TRP GLY ALA SEQRES 16 A 296 ALA ASN ASN VAL PHE THR ASN GLU PHE TYR LEU ASN LEU SEQRES 17 A 296 LEU ASN GLU ASP TRP LYS LEU GLU LYS ASN ASP ALA ASN SEQRES 18 A 296 ASN GLU GLN TRP ASP SER LYS SER GLY TYR MET MET LEU SEQRES 19 A 296 PRO THR ASP TYR SER LEU ILE GLN ASP PRO LYS TYR LEU SEQRES 20 A 296 SER ILE VAL LYS GLU TYR ALA ASN ASP GLN ASP LYS PHE SEQRES 21 A 296 PHE LYS ASP PHE SER LYS ALA PHE GLU LYS LEU LEU GLU SEQRES 22 A 296 ASN GLY ILE THR PHE PRO LYS ASP ALA PRO SER PRO PHE SEQRES 23 A 296 ILE PHE LYS THR LEU GLU GLU GLN GLY LEU HET HEM A 301 43 HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETSYN HEM HEME FORMUL 2 HEM C34 H32 FE N4 O4 FORMUL 3 HOH *202(H2 O) HELIX 1 AA1 SER A 15 ASP A 33 1 19 HELIX 2 AA2 GLU A 35 ILE A 40 1 6 HELIX 3 AA3 TYR A 42 GLY A 55 1 14 HELIX 4 AA4 GLY A 69 ARG A 72 5 4 HELIX 5 AA5 PHE A 73 ASN A 78 1 6 HELIX 6 AA6 ASP A 79 GLY A 84 5 6 HELIX 7 AA7 LEU A 85 PHE A 99 1 15 HELIX 8 AA8 SER A 103 MET A 119 1 17 HELIX 9 AA9 PRO A 134 THR A 138 5 5 HELIX 10 AB1 ASP A 150 ARG A 160 1 11 HELIX 11 AB2 ASN A 164 GLY A 173 1 10 HELIX 12 AB3 ALA A 174 LEU A 177 5 4 HELIX 13 AB4 HIS A 181 GLY A 186 1 6 HELIX 14 AB5 ASN A 200 GLU A 209 1 10 HELIX 15 AB6 LEU A 232 ASP A 241 1 10 HELIX 16 AB7 ASP A 241 ASP A 254 1 14 HELIX 17 AB8 ASP A 254 ASN A 272 1 19 HELIX 18 AB9 LEU A 289 GLY A 293 5 5 SHEET 1 AA1 2 HIS A 6 VAL A 7 0 SHEET 2 AA1 2 ILE A 274 THR A 275 1 O THR A 275 N HIS A 6 SHEET 1 AA2 2 LYS A 179 THR A 180 0 SHEET 2 AA2 2 GLY A 189 PRO A 190 -1 O GLY A 189 N THR A 180 SHEET 1 AA3 3 TRP A 211 LYS A 215 0 SHEET 2 AA3 3 GLU A 221 SER A 225 -1 O GLN A 222 N GLU A 214 SHEET 3 AA3 3 MET A 230 MET A 231 -1 O MET A 231 N TRP A 223 LINK NE2 HIS A 175 FE HEM A 301 1555 1555 2.10 LINK FE HEM A 301 O HOH A 521 1555 1555 2.65 CRYST1 45.143 74.384 101.493 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 0.022152 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013444 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009853 0.00000