HEADER METAL BINDING PROTEIN 09-DEC-25 21DV TITLE CRYSTAL STRUCTURE OF DE NOVO DESIGNED TYPE-I CUPREDOXIN AZ83647 COMPND MOL_ID: 1; COMPND 2 MOLECULE: AZURIN 83647; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: UNIDENTIFIED; SOURCE 3 ORGANISM_TAXID: 32644; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS AZURIN, COPPER BINDING PROTEIN, METAL BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR S.WANG,G.TANG REVDAT 1 11-NOV-26 21DV 0 JRNL AUTH S.WANG,G.TANG,P.ZHENG JRNL TITL AI DE NOVO DESIGN OF COPPER-BINDING PROTEINS WITH DIVERSE JRNL TITL 2 REDOX POTENTIALS JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.21.2_5419 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) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.66 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 20163 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.193 REMARK 3 R VALUE (WORKING SET) : 0.191 REMARK 3 FREE R VALUE : 0.228 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.880 REMARK 3 FREE R VALUE TEST SET COUNT : 983 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 32.6600 - 2.8700 1.00 2908 135 0.1911 0.2194 REMARK 3 2 2.8700 - 2.2800 1.00 2760 147 0.1902 0.2123 REMARK 3 3 2.2800 - 1.9900 1.00 2718 146 0.1729 0.2297 REMARK 3 4 1.9900 - 1.8100 1.00 2718 143 0.1892 0.2352 REMARK 3 5 1.8100 - 1.6800 1.00 2679 151 0.1881 0.2282 REMARK 3 6 1.6800 - 1.5800 1.00 2717 119 0.2334 0.3328 REMARK 3 7 1.5800 - 1.5000 1.00 2680 142 0.2285 0.2455 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) : 0.154 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.595 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 17.96 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 24.93 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 : 0.011 985 REMARK 3 ANGLE : 1.165 1327 REMARK 3 CHIRALITY : 0.079 149 REMARK 3 PLANARITY : 0.008 172 REMARK 3 DIHEDRAL : 17.500 371 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): -3.4126 15.2992 -12.7096 REMARK 3 T TENSOR REMARK 3 T11: 0.1426 T22: 0.0737 REMARK 3 T33: 0.1535 T12: 0.0104 REMARK 3 T13: 0.0216 T23: -0.0028 REMARK 3 L TENSOR REMARK 3 L11: 2.4794 L22: 1.8806 REMARK 3 L33: 1.6267 L12: 0.2467 REMARK 3 L13: -0.2926 L23: 0.4287 REMARK 3 S TENSOR REMARK 3 S11: 0.0412 S12: 0.0890 S13: 0.1414 REMARK 3 S21: -0.2668 S22: 0.0010 S23: 0.0057 REMARK 3 S31: -0.2229 S32: -0.0564 S33: -0.0202 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 21DV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBC ON 17-DEC-25. REMARK 100 THE DEPOSITION ID IS D_1300067051. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-DEC-25 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL02U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97918 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER2 S 9M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : POINTLESS, AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 20215 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 39.450 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 12.60 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 6.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.53 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 1.09800 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.18 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.99 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.05M CALCIUM CHLORIDE, 0.1M BIS-TRIS REMARK 280 PH 7.2, 34% V/V PEG MONOMETHYLETHER 550, VAPOR DIFFUSION, REMARK 280 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 19.09250 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 31.50700 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 25.29850 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 31.50700 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 19.09250 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 25.29850 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 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 GLY A 2 REMARK 465 SER A 3 REMARK 465 GLU A 107 REMARK 465 GLY A 108 REMARK 465 GLU A 109 REMARK 465 GLY A 132 REMARK 465 THR A 133 REMARK 465 HIS A 134 REMARK 465 HIS A 135 REMARK 465 HIS A 136 REMARK 465 HIS A 137 REMARK 465 HIS A 138 REMARK 465 HIS A 139 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 CU A 201 CU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 49 ND1 REMARK 620 2 CYS A 115 SG 131.4 REMARK 620 3 HIS A 120 ND1 107.3 121.4 REMARK 620 N 1 2 DBREF 21DV A 1 139 PDB 21DV 21DV 1 139 SEQRES 1 A 139 MET GLY SER GLY PRO CYS SER VAL ASP ILE THR GLY ASP SEQRES 2 A 139 ASP ASN ASN ASN PHE SER ILE ASN GLU ILE THR VAL PRO SEQRES 3 A 139 LYS SER CYS LYS THR PHE THR VAL ASN LEU THR LYS PRO SEQRES 4 A 139 GLY SER LEU PRO LYS GLU LYS ASN GLY HIS ASN ILE VAL SEQRES 5 A 139 ILE THR LYS LYS GLU ASP LYS ASP ASP VAL VAL GLU GLU SEQRES 6 A 139 GLY GLU LYS ALA GLY PHE GLU ASN ASP TYR LEU LYS PRO SEQRES 7 A 139 ASN ASN PRO LYS VAL ILE ALA HIS THR LYS LEU ILE GLY SEQRES 8 A 139 SER GLY GLU SER ASP SER PHE THR PHE PRO VAL SER LYS SEQRES 9 A 139 LEU LYS GLU GLY GLU GLU TYR THR PHE PHE CYS THR PHE SEQRES 10 A 139 PRO GLY HIS SER LYS LYS MET ASN GLY THR LEU LYS LEU SEQRES 11 A 139 VAL GLY THR HIS HIS HIS HIS HIS HIS HET CU A 201 1 HETNAM CU COPPER (II) ION FORMUL 2 CU CU 2+ FORMUL 3 HOH *76(H2 O) HELIX 1 AA1 ASP A 58 GLY A 70 1 13 HELIX 2 AA2 PHE A 71 ASP A 74 5 4 HELIX 3 AA3 SER A 103 LEU A 105 5 3 SHEET 1 AA1 3 SER A 7 THR A 11 0 SHEET 2 AA1 3 THR A 31 THR A 37 1 O ASN A 35 N ILE A 10 SHEET 3 AA1 3 SER A 95 PRO A 101 -1 O ASP A 96 N LEU A 36 SHEET 1 AA2 5 GLU A 22 PRO A 26 0 SHEET 2 AA2 5 ASN A 125 VAL A 131 1 O THR A 127 N ILE A 23 SHEET 3 AA2 5 TYR A 111 PHE A 114 -1 N PHE A 113 O GLY A 126 SHEET 4 AA2 5 VAL A 52 LYS A 55 -1 N THR A 54 O THR A 112 SHEET 5 AA2 5 ALA A 85 HIS A 86 -1 O ALA A 85 N ILE A 53 SSBOND 1 CYS A 6 CYS A 29 1555 1555 2.04 LINK ND1 HIS A 49 CU CU A 201 1555 1555 2.08 LINK SG CYS A 115 CU CU A 201 1555 1555 2.16 LINK ND1 HIS A 120 CU CU A 201 1555 1555 2.01 CRYST1 38.185 50.597 63.014 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 0.026188 0.000000 0.000000 0.00000 SCALE2 0.000000 0.019764 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015869 0.00000 CONECT 17 189 CONECT 189 17 CONECT 340 968 CONECT 844 968 CONECT 880 968 CONECT 968 340 844 880 MASTER 242 0 1 3 8 0 0 6 1043 1 6 11 END