HEADER OXIDOREDUCTASE/IMMUNE SYSTEM 14-JUL-23 8K3A TITLE SOD1 AND NANOBODY2 COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: SUPEROXIDE DISMUTASE [CU-ZN]; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: SUPEROXIDE DISMUTASE 1,HSOD1; COMPND 5 EC: 1.15.1.1; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: NB2; COMPND 9 CHAIN: B; COMPND 10 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: SOD1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: CAMELUS DROMEDARIUS; SOURCE 10 ORGANISM_TAXID: 9838; SOURCE 11 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 12 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS ANTIBODY COMPLEX, OXIDOREDUCTASE/IMMUNE SYSTEM, OXIDOREDUCTASE-IMMUNE KEYWDS 2 SYSTEM COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR S.CHENG REVDAT 2 30-OCT-24 8K3A 1 REMARK REVDAT 1 17-JUL-24 8K3A 0 JRNL AUTH S.CHENG JRNL TITL SOD1 AND NANOBODY1 COMPLEX JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.74 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.20.1_4487: ???) 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.74 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 49.06 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.390 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 12973 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.235 REMARK 3 R VALUE (WORKING SET) : 0.234 REMARK 3 FREE R VALUE : 0.256 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.850 REMARK 3 FREE R VALUE TEST SET COUNT : 629 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 49.0600 - 4.3500 1.00 3140 163 0.1955 0.2075 REMARK 3 2 4.3500 - 3.4500 1.00 3098 136 0.2270 0.2587 REMARK 3 3 3.4500 - 3.0200 1.00 3069 156 0.2958 0.3260 REMARK 3 4 3.0200 - 2.7400 1.00 3037 174 0.3654 0.4107 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) : 0.350 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 36.080 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 : 0.003 NULL REMARK 3 ANGLE : 0.586 NULL REMARK 3 CHIRALITY : 0.048 309 REMARK 3 PLANARITY : 0.005 388 REMARK 3 DIHEDRAL : 4.795 304 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 8K3A COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBC ON 19-JUL-23. REMARK 100 THE DEPOSITION ID IS D_1300039454. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-OCT-21 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) : 0.979 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER2 X 4M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13011 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.740 REMARK 200 RESOLUTION RANGE LOW (A) : 66.850 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 12.80 REMARK 200 R MERGE (I) : 0.14300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.74 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.89 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 1.53100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 70.29 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.14 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M MAGNESIUM CHLORIDE, 0.1 M REMARK 280 SODIUM, CITRATE PH 5, 15%(W/V) PEG 4000, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 6 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 -X,-Y,Z REMARK 290 5555 Y,-X+Y,Z REMARK 290 6555 X-Y,X,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 -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 0.00000 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 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 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 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1200 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13260 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -6.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 ARG A 69 CZ REMARK 480 ASP A 96 CG REMARK 480 GLU A 100 OE1 REMARK 480 GLU A 132 CD REMARK 480 GLN A 153 C 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 PHE A 64 104.45 -52.58 REMARK 500 ASP A 90 -163.60 -76.71 REMARK 500 LYS A 136 -61.95 -121.36 REMARK 500 LEU B 18 111.29 -160.37 REMARK 500 ARG B 41 117.39 -161.48 REMARK 500 PRO B 44 104.86 -58.98 REMARK 500 GLU B 49 -93.79 -97.57 REMARK 500 SER B 59 31.21 -150.47 REMARK 500 GLU B 68 -115.03 -131.93 REMARK 500 ASP B 118 -78.88 -91.30 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 201 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 63 ND1 REMARK 620 2 HIS A 71 ND1 111.4 REMARK 620 3 HIS A 80 ND1 107.8 119.9 REMARK 620 4 ASP A 83 OD1 114.6 97.7 105.3 REMARK 620 N 1 2 3 DBREF 8K3A A 1 153 UNP P00441 SODC_HUMAN 2 154 DBREF 8K3A B 0 130 PDB 8K3A 8K3A 0 130 SEQRES 1 A 153 ALA THR LYS ALA VAL CYS VAL LEU LYS GLY ASP GLY PRO SEQRES 2 A 153 VAL GLN GLY ILE ILE ASN PHE GLU GLN LYS GLU SER ASN SEQRES 3 A 153 GLY PRO VAL LYS VAL TRP GLY SER ILE LYS GLY LEU THR SEQRES 4 A 153 GLU GLY LEU HIS GLY PHE HIS VAL HIS GLU PHE GLY ASP SEQRES 5 A 153 ASN THR ALA GLY CYS THR SER ALA GLY PRO HIS PHE ASN SEQRES 6 A 153 PRO LEU SER ARG LYS HIS GLY GLY PRO LYS ASP GLU GLU SEQRES 7 A 153 ARG HIS VAL GLY ASP LEU GLY ASN VAL THR ALA ASP LYS SEQRES 8 A 153 ASP GLY VAL ALA ASP VAL SER ILE GLU ASP SER VAL ILE SEQRES 9 A 153 SER LEU SER GLY ASP HIS CYS ILE ILE GLY ARG THR LEU SEQRES 10 A 153 VAL VAL HIS GLU LYS ALA ASP ASP LEU GLY LYS GLY GLY SEQRES 11 A 153 ASN GLU GLU SER THR LYS THR GLY ASN ALA GLY SER ARG SEQRES 12 A 153 LEU ALA CYS GLY VAL ILE GLY ILE ALA GLN SEQRES 1 B 131 SER GLN VAL GLN LEU GLN GLU SER GLY GLY GLY SER VAL SEQRES 2 B 131 GLN ALA GLY GLY SER LEU ARG LEU ALA CYS VAL ALA SER SEQRES 3 B 131 GLY GLY ASP THR ARG PRO TYR ILE THR TYR TRP MET GLY SEQRES 4 B 131 TRP TYR ARG GLN ALA PRO GLY LYS GLU ARG GLU GLY VAL SEQRES 5 B 131 ALA THR ILE TYR THR GLY GLY SER GLY THR TYR TYR SER SEQRES 6 B 131 ASP SER VAL GLU GLY ARG PHE THR ILE SER GLN ASP LYS SEQRES 7 B 131 ALA GLN ARG THR VAL TYR LEU GLN MET ASN ASP LEU LYS SEQRES 8 B 131 PRO GLU ASP THR ALA MET TYR TYR CYS ALA ALA GLY ASN SEQRES 9 B 131 GLY ALA LEU PRO PRO GLY ARG ARG LEU SER PRO GLN ASN SEQRES 10 B 131 MET ASP THR TRP GLY PRO GLY THR GLN VAL THR VAL SER SEQRES 11 B 131 SER HET ZN A 201 1 HETNAM ZN ZINC ION FORMUL 3 ZN ZN 2+ FORMUL 4 HOH *(H2 O) HELIX 1 AA1 ALA A 55 GLY A 61 5 7 HELIX 2 AA2 LYS B 90 THR B 94 5 5 HELIX 3 AA3 GLY B 109 SER B 113 5 5 SHEET 1 AA1 5 ALA A 95 ASP A 101 0 SHEET 2 AA1 5 VAL A 29 LYS A 36 -1 N VAL A 31 O ILE A 99 SHEET 3 AA1 5 GLN A 15 GLN A 22 -1 N ASN A 19 O TRP A 32 SHEET 4 AA1 5 THR A 2 LYS A 9 -1 N THR A 2 O GLN A 22 SHEET 5 AA1 5 GLY A 150 ILE A 151 -1 O GLY A 150 N VAL A 5 SHEET 1 AA2 4 ASP A 83 ALA A 89 0 SHEET 2 AA2 4 GLY A 41 VAL A 47 -1 N GLY A 41 O ALA A 89 SHEET 3 AA2 4 THR A 116 HIS A 120 -1 O VAL A 118 N HIS A 46 SHEET 4 AA2 4 ARG A 143 VAL A 148 -1 O GLY A 147 N LEU A 117 SHEET 1 AA3 4 GLN B 3 SER B 7 0 SHEET 2 AA3 4 LEU B 20 SER B 25 -1 O SER B 25 N GLN B 3 SHEET 3 AA3 4 THR B 81 MET B 86 -1 O LEU B 84 N LEU B 20 SHEET 4 AA3 4 PHE B 71 ASP B 76 -1 N THR B 72 O GLN B 85 SHEET 1 AA4 3 SER B 11 GLN B 13 0 SHEET 2 AA4 3 THR B 124 SER B 129 1 O SER B 129 N VAL B 12 SHEET 3 AA4 3 ALA B 95 TYR B 97 -1 N ALA B 95 O VAL B 126 SHEET 1 AA5 5 THR B 61 TYR B 63 0 SHEET 2 AA5 5 ALA B 52 TYR B 55 -1 N THR B 53 O TYR B 62 SHEET 3 AA5 5 TYR B 35 TRP B 39 -1 N MET B 37 O ILE B 54 SHEET 4 AA5 5 CYS B 99 ASN B 103 -1 O ALA B 100 N GLY B 38 SHEET 5 AA5 5 THR B 119 TRP B 120 -1 O THR B 119 N ALA B 101 SSBOND 1 CYS A 57 CYS A 146 1555 1555 2.03 LINK ND1 HIS A 63 ZN ZN A 201 1555 1555 2.30 LINK ND1 HIS A 71 ZN ZN A 201 1555 1555 2.30 LINK ND1 HIS A 80 ZN ZN A 201 1555 1555 2.30 LINK OD1 ASP A 83 ZN ZN A 201 1555 1555 1.92 CRYST1 113.290 113.290 66.849 90.00 90.00 120.00 P 6 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 0.008827 0.005096 0.000000 0.00000 SCALE2 0.000000 0.010192 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014959 0.00000