HEADER METAL BINDING PROTEIN 21-JUL-22 8DRL TITLE ZN(II)-BOUND B2 DIMER (H60/H100/H104) FORMED IN CU(II)//ZN(II) (M1 // TITLE 2 M2) CONDITION COMPND MOL_ID: 1; COMPND 2 MOLECULE: SOLUBLE CYTOCHROME B562; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: CYTOCHROME B-562; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 GENE: CYBC; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS TRINUCLEAR, SELECTIVITY, METAL BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR T.S.CHOI,F.A.TEZCAN REVDAT 3 09-OCT-24 8DRL 1 REMARK REVDAT 2 18-OCT-23 8DRL 1 REMARK REVDAT 1 12-OCT-22 8DRL 0 JRNL AUTH T.S.CHOI,F.A.TEZCAN JRNL TITL DESIGN OF A FLEXIBLE, ZN-SELECTIVE PROTEIN SCAFFOLD THAT JRNL TITL 2 DISPLAYS ANTI-IRVING-WILLIAMS BEHAVIOR. JRNL REF J.AM.CHEM.SOC. V. 144 18090 2022 JRNL REFN ESSN 1520-5126 JRNL PMID 36154053 JRNL DOI 10.1021/JACS.2C08050 REMARK 2 REMARK 2 RESOLUTION. 1.65 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.15.2_3472 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) : 1.65 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.64 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.9 REMARK 3 NUMBER OF REFLECTIONS : 15118 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.183 REMARK 3 R VALUE (WORKING SET) : 0.181 REMARK 3 FREE R VALUE : 0.202 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.030 REMARK 3 FREE R VALUE TEST SET COUNT : 2790 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 39.6400 - 4.4800 0.98 1266 134 0.1435 0.1681 REMARK 3 2 4.4800 - 3.5500 1.00 1270 151 0.1642 0.1635 REMARK 3 3 3.5500 - 3.1000 0.98 1257 137 0.1799 0.2162 REMARK 3 4 3.1000 - 2.8200 0.99 1244 141 0.1919 0.2066 REMARK 3 5 2.8200 - 2.6200 1.00 1265 144 0.1937 0.2102 REMARK 3 6 2.6200 - 2.4600 0.99 1271 142 0.1861 0.1864 REMARK 3 7 2.4600 - 2.3400 0.99 1258 136 0.1823 0.2095 REMARK 3 8 2.3400 - 2.2400 0.97 1248 137 0.2044 0.2071 REMARK 3 9 2.2400 - 2.1500 0.98 1259 146 0.1764 0.1881 REMARK 3 10 2.1500 - 2.0800 0.99 1263 142 0.1773 0.2201 REMARK 3 11 2.0800 - 2.0100 0.98 1233 133 0.2015 0.2219 REMARK 3 12 2.0100 - 1.9600 0.98 1273 137 0.1935 0.2720 REMARK 3 13 1.9600 - 1.9000 0.97 1254 135 0.2087 0.2440 REMARK 3 14 1.9000 - 1.8600 0.95 1211 137 0.2069 0.2244 REMARK 3 15 1.8600 - 1.8200 0.97 1249 135 0.1868 0.2477 REMARK 3 16 1.8200 - 1.7800 0.97 1221 135 0.1848 0.2070 REMARK 3 17 1.7800 - 1.7400 0.97 1240 148 0.1913 0.2098 REMARK 3 18 1.7400 - 1.7100 0.97 1254 139 0.1926 0.2203 REMARK 3 19 1.7100 - 1.6800 0.97 1240 137 0.2018 0.2332 REMARK 3 20 1.6800 - 1.6500 0.98 1261 144 0.1978 0.2208 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL 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) : 0.146 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.190 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 18.17 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.58 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 : 0.007 891 REMARK 3 ANGLE : 0.845 1220 REMARK 3 CHIRALITY : 0.041 125 REMARK 3 PLANARITY : 0.005 161 REMARK 3 DIHEDRAL : 10.774 736 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 8DRL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 21-JUL-22. REMARK 100 THE DEPOSITION ID IS D_1000267255. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-OCT-20 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 9 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL9-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.27159 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : IMOSFLM REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15118 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.650 REMARK 200 RESOLUTION RANGE LOW (A) : 39.640 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 200 DATA REDUNDANCY : 2.000 REMARK 200 R MERGE (I) : 0.04037 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.4600 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.65 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.71 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.12270 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 5.030 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: 2BC5 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.16 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.57 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG3350 24%, CHES 100 MM, PH 9, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 2 21 21 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,Y+1/2,-Z+1/2 REMARK 290 4555 -X,-Y+1/2,Z+1/2 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 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 26.20500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 29.31500 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 26.20500 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 29.31500 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4020 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10870 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -230.0 KCAL/MOL 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 350 BIOMT1 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 52.41000 REMARK 350 BIOMT3 2 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 ZN ZN A 202 LIES ON A SPECIAL POSITION. 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 LYS A 15 CE NZ REMARK 470 LYS A 47 CG CD CE NZ 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 OD2 ASP A 50 O HOH A 301 2.17 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 ZN A 204 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 4 OE1 REMARK 620 2 GLU A 8 OE1 117.9 REMARK 620 3 GLU A 86 OE2 113.6 4.8 REMARK 620 4 HEC A 201 O1A 110.9 109.0 109.6 REMARK 620 N 1 2 3 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 MET A 7 SD REMARK 620 2 HEC A 201 NA 88.1 REMARK 620 3 HEC A 201 NB 87.3 89.7 REMARK 620 4 HEC A 201 NC 93.8 177.7 89.0 REMARK 620 5 HEC A 201 ND 92.7 92.1 178.2 89.2 REMARK 620 6 HIS A 102 NE2 172.5 87.7 86.5 90.3 93.7 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 203 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 57 OE1 REMARK 620 2 HIS A 60 ND1 116.4 REMARK 620 3 HIS A 63 NE2 110.8 19.4 REMARK 620 4 HIS A 104 NE2 110.9 107.6 125.3 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 202 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 60 NE2 REMARK 620 2 HIS A 60 NE2 0.0 REMARK 620 3 HOH A 393 O 96.7 96.7 REMARK 620 4 HOH A 393 O 98.8 98.8 154.2 REMARK 620 N 1 2 3 DBREF 8DRL A 1 106 UNP P0ABE7 C562_ECOLX 23 128 SEQADV 8DRL TRP A 59 UNP P0ABE7 LYS 81 CONFLICT SEQADV 8DRL HIS A 60 UNP P0ABE7 ASP 82 ENGINEERED MUTATION SEQADV 8DRL CYS A 96 UNP P0ABE7 THR 118 CONFLICT SEQADV 8DRL CYS A 98 UNP P0ABE7 ARG 120 CONFLICT SEQADV 8DRL HIS A 100 UNP P0ABE7 ALA 122 ENGINEERED MUTATION SEQADV 8DRL CYS A 101 UNP P0ABE7 TYR 123 CONFLICT SEQADV 8DRL HIS A 104 UNP P0ABE7 LYS 126 ENGINEERED MUTATION SEQRES 1 A 106 ALA ASP LEU 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 THR LYS MET ARG ALA ALA ALA LEU ASP SEQRES 4 A 106 ALA GLN LYS ALA THR PRO PRO LYS LEU GLU ASP LYS SER SEQRES 5 A 106 PRO ASP SER PRO GLU MET TRP HIS PHE ARG HIS GLY PHE SEQRES 6 A 106 ASP ILE LEU VAL GLY GLN ILE ASP ASP ALA LEU LYS LEU SEQRES 7 A 106 ALA ASN GLU GLY LYS VAL LYS GLU ALA GLN ALA ALA ALA SEQRES 8 A 106 GLU GLN LEU LYS CYS THR CYS ASN HIS CYS HIS GLN HIS SEQRES 9 A 106 TYR ARG HET HEC A 201 43 HET ZN A 202 1 HET ZN A 203 1 HET ZN A 204 1 HETNAM HEC HEME C HETNAM ZN ZINC ION FORMUL 2 HEC C34 H34 FE N4 O4 FORMUL 3 ZN 3(ZN 2+) FORMUL 6 HOH *130(H2 O) HELIX 1 AA1 ASP A 2 ALA A 20 1 19 HELIX 2 AA2 ASN A 22 GLN A 41 1 20 HELIX 3 AA3 SER A 55 GLU A 81 1 27 HELIX 4 AA4 LYS A 83 GLN A 93 1 11 HELIX 5 AA5 LEU A 94 ARG A 106 1 13 SSBOND 1 CYS A 96 CYS A 96 1555 2565 2.04 LINK SG CYS A 98 CAB HEC A 201 1555 1555 1.78 LINK OE1 GLU A 4 ZN ZN A 204 1555 1555 1.98 LINK SD MET A 7 FE HEC A 201 1555 1555 2.39 LINK OE1 GLU A 8 ZN ZN A 204 1555 1555 1.98 LINK OE1 GLU A 57 ZN ZN A 203 1555 2565 2.03 LINK NE2 HIS A 60 ZN ZN A 202 1555 1555 2.00 LINK NE2 HIS A 60 ZN ZN A 202 1555 2565 2.00 LINK ND1 HIS A 60 ZN ZN A 203 1555 2565 1.99 LINK NE2 HIS A 63 ZN ZN A 203 1555 1555 2.13 LINK OE2 GLU A 86 ZN ZN A 204 1555 4555 2.04 LINK NE2 HIS A 102 FE HEC A 201 1555 1555 2.11 LINK NE2 HIS A 104 ZN ZN A 203 1555 2565 2.07 LINK O1A HEC A 201 ZN ZN A 204 1555 1555 1.94 LINK ZN ZN A 202 O HOH A 393 1555 1555 2.50 LINK ZN ZN A 202 O HOH A 393 1555 2565 2.50 CRYST1 39.640 52.410 58.630 90.00 90.00 90.00 P 2 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 0.025227 0.000000 0.000000 0.00000 SCALE2 0.000000 0.019080 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017056 0.00000