HEADER DE NOVO PROTEIN 20-JUN-22 8DEL TITLE TRIMERIC HEME-FREE CYTOCHROME VARIANT APOCYT-TRICYT3 COMPND MOL_ID: 1; COMPND 2 MOLECULE: SOLUBLE CYTOCHROME B562; COMPND 3 CHAIN: A, B, C; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI BL21(DE3); SOURCE 3 ORGANISM_TAXID: 469008; SOURCE 4 GENE: CYBC; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS APO CYTOCHROME B562, ENGINEERED PROTEIN, DE NOVO PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR A.M.HOFFNAGLE,V.H.ENG,F.A.TEZCAN REVDAT 4 18-OCT-23 8DEL 1 REMARK REVDAT 3 12-OCT-22 8DEL 1 JRNL REVDAT 2 05-OCT-22 8DEL 1 JRNL REVDAT 1 06-JUL-22 8DEL 0 JRNL AUTH A.M.HOFFNAGLE,V.H.ENG,U.MARKEL,F.A.TEZCAN JRNL TITL COMPUTATIONALLY GUIDED REDESIGN OF A HEME-FREE CYTOCHROME JRNL TITL 2 WITH NATIVE-LIKE STRUCTURE AND STABILITY. JRNL REF BIOCHEMISTRY V. 61 2063 2022 JRNL REFN ISSN 0006-2960 JRNL PMID 36106943 JRNL DOI 10.1021/ACS.BIOCHEM.2C00369 REMARK 2 REMARK 2 RESOLUTION. 2.56 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.17 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) : 2.56 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.80 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 9887 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.210 REMARK 3 R VALUE (WORKING SET) : 0.203 REMARK 3 FREE R VALUE : 0.279 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.860 REMARK 3 FREE R VALUE TEST SET COUNT : 1901 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 45.8000 - 6.1600 0.99 1249 123 0.1483 0.1874 REMARK 3 2 6.1600 - 4.9000 1.00 1209 149 0.2007 0.3002 REMARK 3 3 4.8900 - 4.2800 1.00 1269 143 0.1694 0.2015 REMARK 3 4 4.2700 - 3.8900 1.00 1252 132 0.1771 0.2636 REMARK 3 5 3.8800 - 3.6100 1.00 1246 127 0.1903 0.2660 REMARK 3 6 3.6100 - 3.3900 1.00 1231 133 0.1964 0.3009 REMARK 3 7 3.3900 - 3.2200 1.00 1268 141 0.2247 0.2911 REMARK 3 8 3.2200 - 3.0800 1.00 1203 143 0.2435 0.3662 REMARK 3 9 3.0800 - 2.9600 1.00 1243 135 0.2507 0.3501 REMARK 3 10 2.9600 - 2.8600 1.00 1273 127 0.2432 0.3370 REMARK 3 11 2.8600 - 2.7700 1.00 1201 133 0.2755 0.3915 REMARK 3 12 2.7700 - 2.6900 1.00 1277 156 0.2667 0.3624 REMARK 3 13 2.6900 - 2.6200 1.00 1194 127 0.2765 0.3631 REMARK 3 14 2.6200 - 2.5600 0.98 1259 132 0.2803 0.3603 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 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) : NULL REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 33.050 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 53.10 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 : 0.009 2575 REMARK 3 ANGLE : 1.103 3473 REMARK 3 CHIRALITY : 0.056 374 REMARK 3 PLANARITY : 0.008 456 REMARK 3 DIHEDRAL : 25.547 988 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 8DEL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 21-JUN-22. REMARK 100 THE DEPOSITION ID IS D_1000266480. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-MAR-21 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.5 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 : BRUKER AXS MICROSTAR REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : APEX II CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : APEX REMARK 200 DATA SCALING SOFTWARE : APEX REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9904 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.560 REMARK 200 RESOLUTION RANGE LOW (A) : 45.800 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 8.900 REMARK 200 R MERGE (I) : 0.06400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.56 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.65 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.4 REMARK 200 DATA REDUNDANCY IN SHELL : 5.30 REMARK 200 R MERGE FOR SHELL (I) : 0.53300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.200 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: 6WZC REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.93 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.16 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25% PEG 1500, 200 MM (NH4)2SO4, 100 MM REMARK 280 BIS-TRIS PH 5.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K 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 21.88900 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 38.53800 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 21.88900 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 38.53800 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3960 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15520 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -74.0 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 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 A 329 LIES ON A SPECIAL POSITION. REMARK 375 HOH C 228 LIES ON A SPECIAL POSITION. 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 O HOH C 203 O HOH C 211 1.98 REMARK 500 OE1 GLN C 93 O HOH C 201 2.11 REMARK 500 O HOH C 216 O HOH C 218 2.13 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 LYS C 83 79.21 -101.03 REMARK 500 LYS C 104 -46.60 75.68 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 C 228 DISTANCE = 7.41 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 ZN A 201 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 73 NE2 REMARK 620 2 HIS A 77 NE2 79.3 REMARK 620 3 HIS B 73 NE2 88.8 147.2 REMARK 620 4 HIS B 77 NE2 120.4 76.1 84.1 REMARK 620 5 HIS C 73 NE2 86.1 117.3 91.9 152.9 REMARK 620 N 1 2 3 4 DBREF 8DEL A 1 106 PDB 8DEL 8DEL 1 106 DBREF 8DEL B 1 106 PDB 8DEL 8DEL 1 106 DBREF 8DEL C 1 106 PDB 8DEL 8DEL 1 106 SEQRES 1 A 106 ALA ASP TRP GLU ASP ASN MET GLU THR LEU ASN ASP ASN SEQRES 2 A 106 LEU LYS VAL ILE GLU LYS ALA ASP ASN ALA ALA GLN VAL SEQRES 3 A 106 LYS ASP ALA LEU LYS LYS MET ARG LYS ALA ALA LEU ASP SEQRES 4 A 106 ALA LYS LYS ALA THR PRO PRO LYS LEU GLU ASP LYS SER SEQRES 5 A 106 PRO ALA SER PRO GLU MET ILE ASP PHE ARG VAL GLY PHE SEQRES 6 A 106 ASP GLU LEU ALA TRP GLU ILE HIS ASP ALA ALA HIS LEU SEQRES 7 A 106 ALA LYS GLU GLY LYS VAL LYS GLU ALA GLN ALA ALA ALA SEQRES 8 A 106 GLU GLN LEU LYS THR THR VAL ASN ALA HIS TRP GLN LYS SEQRES 9 A 106 TYR ARG SEQRES 1 B 106 ALA ASP TRP GLU ASP ASN MET GLU THR LEU ASN ASP ASN SEQRES 2 B 106 LEU LYS VAL ILE GLU LYS ALA ASP ASN ALA ALA GLN VAL SEQRES 3 B 106 LYS ASP ALA LEU LYS LYS MET ARG LYS ALA ALA LEU ASP SEQRES 4 B 106 ALA LYS LYS ALA THR PRO PRO LYS LEU GLU ASP LYS SER SEQRES 5 B 106 PRO ALA SER PRO GLU MET ILE ASP PHE ARG VAL GLY PHE SEQRES 6 B 106 ASP GLU LEU ALA TRP GLU ILE HIS ASP ALA ALA HIS LEU SEQRES 7 B 106 ALA LYS GLU GLY LYS VAL LYS GLU ALA GLN ALA ALA ALA SEQRES 8 B 106 GLU GLN LEU LYS THR THR VAL ASN ALA HIS TRP GLN LYS SEQRES 9 B 106 TYR ARG SEQRES 1 C 106 ALA ASP TRP GLU ASP ASN MET GLU THR LEU ASN ASP ASN SEQRES 2 C 106 LEU LYS VAL ILE GLU LYS ALA ASP ASN ALA ALA GLN VAL SEQRES 3 C 106 LYS ASP ALA LEU LYS LYS MET ARG LYS ALA ALA LEU ASP SEQRES 4 C 106 ALA LYS LYS ALA THR PRO PRO LYS LEU GLU ASP LYS SER SEQRES 5 C 106 PRO ALA SER PRO GLU MET ILE ASP PHE ARG VAL GLY PHE SEQRES 6 C 106 ASP GLU LEU ALA TRP GLU ILE HIS ASP ALA ALA HIS LEU SEQRES 7 C 106 ALA LYS GLU GLY LYS VAL LYS GLU ALA GLN ALA ALA ALA SEQRES 8 C 106 GLU GLN LEU LYS THR THR VAL ASN ALA HIS TRP GLN LYS SEQRES 9 C 106 TYR ARG HET ZN A 201 1 HET MG A 202 1 HET MG A 203 1 HETNAM ZN ZINC ION HETNAM MG MAGNESIUM ION FORMUL 4 ZN ZN 2+ FORMUL 5 MG 2(MG 2+) FORMUL 7 HOH *105(H2 O) HELIX 1 AA1 ASP A 2 ALA A 20 1 19 HELIX 2 AA2 ASN A 22 LYS A 41 1 20 HELIX 3 AA3 PRO A 45 GLU A 49 5 5 HELIX 4 AA4 SER A 55 GLU A 81 1 27 HELIX 5 AA5 LYS A 83 TYR A 105 1 23 HELIX 6 AA6 ASP B 2 ALA B 20 1 19 HELIX 7 AA7 ASN B 22 LYS B 41 1 20 HELIX 8 AA8 SER B 55 GLY B 82 1 28 HELIX 9 AA9 LYS B 83 ARG B 106 1 24 HELIX 10 AB1 ASP C 2 ALA C 20 1 19 HELIX 11 AB2 ASN C 22 LYS C 41 1 20 HELIX 12 AB3 PRO C 45 GLU C 49 5 5 HELIX 13 AB4 SER C 55 GLU C 81 1 27 HELIX 14 AB5 LYS C 83 ARG C 106 1 24 LINK NE2 HIS A 73 ZN ZN A 201 1555 1555 2.19 LINK NE2 HIS A 77 ZN ZN A 201 1555 1555 2.31 LINK ZN ZN A 201 NE2 HIS B 73 1555 1555 2.13 LINK ZN ZN A 201 NE2 HIS B 77 1555 1555 2.37 LINK ZN ZN A 201 NE2 HIS C 73 1555 1555 2.19 LINK MG MG A 202 O HOH A 319 1555 1555 2.73 CRYST1 43.778 77.076 92.653 90.00 98.69 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 0.022843 0.000000 0.003491 0.00000 SCALE2 0.000000 0.012974 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010918 0.00000