HEADER METAL BINDING PROTEIN 13-AUG-24 9GGO TITLE STRAND-SWAPPED DIMER OF ENGINEERED COPPER BINDING SH3-LIKE PROTEIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: SH3-LIKE PROTEIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 4 ORGANISM_TAXID: 9606 KEYWDS PROTEIN DESIGN, METAL BINDING SITE, SH3-LIKE DOMAIN, METAL BINDING KEYWDS 2 PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR M.SCHWAN,J.KOPP,I.SINNING REVDAT 2 05-FEB-25 9GGO 1 JRNL REVDAT 1 15-JAN-25 9GGO 0 JRNL AUTH F.R.HAGE,M.SCHWAN,M.R.CONDE GONZALEZ,J.HUBER,S.GERMER, JRNL AUTH 2 M.MACRI,J.KOPP,I.SINNING,F.THOMAS JRNL TITL STRAND-SWAPPED SH3 DOMAIN DIMER WITH SUPEROXIDE DISMUTASE JRNL TITL 2 ACTIVITY. JRNL REF ACS CENT.SCI. V. 11 157 2025 JRNL REFN ESSN 2374-7951 JRNL PMID 39866698 JRNL DOI 10.1021/ACSCENTSCI.4C01347 REMARK 2 REMARK 2 RESOLUTION. 2.00 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.61 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 14168 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.205 REMARK 3 R VALUE (WORKING SET) : 0.203 REMARK 3 FREE R VALUE : 0.227 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.980 REMARK 3 FREE R VALUE TEST SET COUNT : 705 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 37.6100 - 3.4200 1.00 2705 129 0.1500 0.1844 REMARK 3 2 3.4200 - 2.7200 1.00 2688 114 0.2093 0.1925 REMARK 3 3 2.7100 - 2.3700 1.00 2689 166 0.2759 0.3211 REMARK 3 4 2.3700 - 2.1600 1.00 2640 186 0.3094 0.3057 REMARK 3 5 2.1500 - 2.0000 1.00 2741 110 0.3375 0.3532 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) : 0.180 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 36.502 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 37.98 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 48.01 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 : 0.004 497 REMARK 3 ANGLE : 0.640 664 REMARK 3 CHIRALITY : 0.044 68 REMARK 3 PLANARITY : 0.005 87 REMARK 3 DIHEDRAL : 15.203 190 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1 THROUGH 11 ) REMARK 3 ORIGIN FOR THE GROUP (A): -26.6200 17.1319 -17.1183 REMARK 3 T TENSOR REMARK 3 T11: 0.3264 T22: 0.3903 REMARK 3 T33: 0.4076 T12: -0.0084 REMARK 3 T13: 0.0209 T23: -0.0316 REMARK 3 L TENSOR REMARK 3 L11: 0.1386 L22: 0.1520 REMARK 3 L33: 0.7959 L12: -0.1445 REMARK 3 L13: -0.0972 L23: 0.1165 REMARK 3 S TENSOR REMARK 3 S11: 0.0603 S12: -0.2682 S13: 0.0606 REMARK 3 S21: 0.0160 S22: -0.0145 S23: 0.0919 REMARK 3 S31: -0.3736 S32: -0.6733 S33: -0.0015 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 12 THROUGH 16 ) REMARK 3 ORIGIN FOR THE GROUP (A): -10.4763 12.8862 -21.8797 REMARK 3 T TENSOR REMARK 3 T11: 0.6078 T22: 0.5931 REMARK 3 T33: 0.5706 T12: 0.0176 REMARK 3 T13: 0.1218 T23: -0.0007 REMARK 3 L TENSOR REMARK 3 L11: 0.1806 L22: 0.1046 REMARK 3 L33: 0.0518 L12: 0.1285 REMARK 3 L13: -0.0580 L23: -0.0630 REMARK 3 S TENSOR REMARK 3 S11: 0.2112 S12: 0.2175 S13: 0.1290 REMARK 3 S21: -0.1283 S22: 0.1535 S23: -0.2538 REMARK 3 S31: -0.0488 S32: 0.1078 S33: -0.0009 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 17 THROUGH 31 ) REMARK 3 ORIGIN FOR THE GROUP (A): -3.7344 27.7386 -26.0333 REMARK 3 T TENSOR REMARK 3 T11: 0.3673 T22: 0.4779 REMARK 3 T33: 0.3966 T12: -0.0574 REMARK 3 T13: -0.0014 T23: 0.0181 REMARK 3 L TENSOR REMARK 3 L11: 0.1485 L22: 0.0753 REMARK 3 L33: 0.2070 L12: 0.1046 REMARK 3 L13: -0.1764 L23: -0.1154 REMARK 3 S TENSOR REMARK 3 S11: -0.0167 S12: 0.4237 S13: 0.0026 REMARK 3 S21: -0.1696 S22: 0.0947 S23: -0.0132 REMARK 3 S31: 0.0717 S32: -0.0950 S33: -0.0001 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 32 THROUGH 58 ) REMARK 3 ORIGIN FOR THE GROUP (A): -21.1174 19.5281 -16.8503 REMARK 3 T TENSOR REMARK 3 T11: 0.4023 T22: 0.4548 REMARK 3 T33: 0.3453 T12: 0.0049 REMARK 3 T13: -0.0046 T23: 0.0477 REMARK 3 L TENSOR REMARK 3 L11: 0.1722 L22: 0.3346 REMARK 3 L33: 0.2798 L12: -0.0123 REMARK 3 L13: 0.1050 L23: 0.0758 REMARK 3 S TENSOR REMARK 3 S11: -0.0443 S12: -0.0592 S13: 0.1384 REMARK 3 S21: 0.1363 S22: -0.0787 S23: -0.0463 REMARK 3 S31: -0.1943 S32: -0.0141 S33: -0.0003 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 9GGO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 13-AUG-24. REMARK 100 THE DEPOSITION ID IS D_1292140532. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-SEP-23 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID23-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.3694 REMARK 200 MONOCHROMATOR : SI(1,1,1) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER2 S 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS 20230630 REMARK 200 DATA SCALING SOFTWARE : AIMLESS 1.12.16 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15348 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 37.610 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 20.90 REMARK 200 R MERGE (I) : 0.16200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.05 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 2.81400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 2.8.3 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 69.06 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.98 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: RESERVOIR: 1.26 M AMMONIUM SULFATE, REMARK 280 0.1 M CHES PH 9.5, 0.2 M SODIUM CHLORIDE. DROPS CONTAINED 300 NL REMARK 280 RESERVOIR SOLUTION AND 300 NL CONCENTRATED PROTEIN., PH 8.5, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 291.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 19.59267 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 39.18533 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 39.18533 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 19.59267 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 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 350 BIOMT2 2 -0.866025 0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 -39.18533 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 HIS A 13 -176.65 -179.60 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 CU A 101 CU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 10 NE2 REMARK 620 2 HIS A 13 NE2 112.5 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CU A 102 CU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 15 OE1 REMARK 620 2 GLU A 17 OE2 41.8 REMARK 620 3 HIS A 50 NE2 130.3 97.4 REMARK 620 N 1 2 DBREF 9GGO A 1 58 PDB 9GGO 9GGO 1 58 SEQRES 1 A 58 ALA GLU TYR VAL ARG ALA LEU PHE ASP HIS THR GLY HIS SEQRES 2 A 58 ASP GLU GLN GLU LEU PRO PHE LYS LYS GLY GLU ILE LEU SEQRES 3 A 58 ARG ILE ARG ASP LYS PRO GLU GLU GLN LEU TRP ASN ALA SEQRES 4 A 58 GLU ASN VAL GLU GLY LYS ARG GLY LEU ILE HIS VAL VAL SEQRES 5 A 58 LEU VAL GLU LYS TYR GLY HET CU A 101 1 HET CU A 102 1 HET EDO A 103 10 HET EDO A 104 10 HETNAM CU COPPER (II) ION HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 2 CU 2(CU 2+) FORMUL 4 EDO 2(C2 H6 O2) FORMUL 6 HOH *20(H2 O) HELIX 1 AA1 LYS A 31 GLU A 34 5 4 SHEET 1 AA1 2 VAL A 4 ALA A 6 0 SHEET 2 AA1 2 VAL A 54 LYS A 56 -1 O GLU A 55 N ARG A 5 SHEET 1 AA2 2 LEU A 36 GLU A 40 0 SHEET 2 AA2 2 ARG A 46 HIS A 50 -1 O GLY A 47 N ALA A 39 LINK NE2 HIS A 10 CU CU A 101 1555 1555 2.06 LINK NE2 HIS A 13 CU CU A 101 1555 1555 2.15 LINK OE1 GLU A 15 CU CU A 102 1555 1555 2.55 LINK OE2 GLU A 17 CU CU A 102 1555 6554 2.32 LINK NE2 HIS A 50 CU CU A 102 1555 1555 2.08 CRYST1 56.509 56.509 58.778 90.00 90.00 120.00 P 31 2 1 6 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 0.017696 0.010217 0.000000 0.00000 SCALE2 0.000000 0.020434 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017013 0.00000 CONECT 86 483 CONECT 107 483 CONECT 123 484 CONECT 418 484 CONECT 483 86 107 CONECT 484 123 418 CONECT 485 486 487 489 490 CONECT 486 485 491 CONECT 487 485 488 492 493 CONECT 488 487 494 CONECT 489 485 CONECT 490 485 CONECT 491 486 CONECT 492 487 CONECT 493 487 CONECT 494 488 CONECT 495 496 497 499 500 CONECT 496 495 501 CONECT 497 495 498 502 503 CONECT 498 497 504 CONECT 499 495 CONECT 500 495 CONECT 501 496 CONECT 502 497 CONECT 503 497 CONECT 504 498 MASTER 301 0 4 1 4 0 0 6 511 1 26 5 END