HEADER DE NOVO PROTEIN 07-JUL-21 7FAO TITLE TOP7 SURFACE MUTANT K42A Q43A K46A K57S K58S, AND I68R COMPND MOL_ID: 1; COMPND 2 MOLECULE: TOP7 SURFACE MUTANT; COMPND 3 CHAIN: A, C; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: UNIDENTIFIED; SOURCE 3 ORGANISM_TAXID: 32644; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) KEYWDS TOP7, SURFACE MUTANT, DE NOVO PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR Y.ITO,K.MAKABE REVDAT 2 29-NOV-23 7FAO 1 REMARK REVDAT 1 18-MAY-22 7FAO 0 JRNL AUTH Y.ITO,T.ARAKI,S.SHIGA,H.KONNO,K.MAKABE JRNL TITL SURFACE ENGINEERING OF TOP7 TO FACILITATE STRUCTURE JRNL TITL 2 DETERMINATION. JRNL REF INT J MOL SCI V. 23 2022 JRNL REFN ESSN 1422-0067 JRNL PMID 35054886 JRNL DOI 10.3390/IJMS23020701 REMARK 2 REMARK 2 RESOLUTION. 1.43 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.17.1-3660 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) : 1.43 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.91 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 3 NUMBER OF REFLECTIONS : 29515 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 : 0.242 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.700 REMARK 3 FREE R VALUE TEST SET COUNT : 1387 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 19.9100 - 3.0800 0.98 2826 140 0.1680 0.2075 REMARK 3 2 3.0800 - 2.4400 0.98 2799 137 0.2105 0.2168 REMARK 3 3 2.4400 - 2.1400 0.98 2808 139 0.1938 0.2543 REMARK 3 4 2.1400 - 1.9400 0.98 2779 137 0.2110 0.2686 REMARK 3 5 1.9400 - 1.8000 0.99 2826 139 0.2264 0.2856 REMARK 3 6 1.8000 - 1.7000 0.98 2765 138 0.2391 0.2972 REMARK 3 7 1.7000 - 1.6100 0.99 2834 140 0.2454 0.2915 REMARK 3 8 1.6100 - 1.5400 0.99 2830 137 0.2723 0.3143 REMARK 3 9 1.5400 - 1.4800 0.99 2843 141 0.2929 0.3525 REMARK 3 10 1.4800 - 1.4300 0.99 2818 139 0.3372 0.3604 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) : 0.202 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 28.900 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 20.49 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 29.04 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 : 0.005 1530 REMARK 3 ANGLE : 0.731 2071 REMARK 3 CHIRALITY : 0.071 245 REMARK 3 PLANARITY : 0.004 271 REMARK 3 DIHEDRAL : 13.377 208 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 7FAO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 13-JUL-21. REMARK 100 THE DEPOSITION ID IS D_1300023067. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-MAY-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 : PHOTON FACTORY REMARK 200 BEAMLINE : BL-5A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 29603 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.430 REMARK 200 RESOLUTION RANGE LOW (A) : 19.910 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 200 DATA REDUNDANCY : 3.200 REMARK 200 R MERGE (I) : 0.03400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.43 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.48 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 3.20 REMARK 200 R MERGE FOR SHELL (I) : 0.49500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 1QYS REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 35.75 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.91 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 8000, SODIUM CACODYLATE, MAGNESIUM REMARK 280 ACETATE, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 292K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 43.14900 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 5370 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 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 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 90 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 5360 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -5.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 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 GLY A -1 REMARK 465 GLY C -1 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 ASN C 13 71.57 51.76 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 MG A 101 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 35 OE2 REMARK 620 2 HOH A 213 O 89.0 REMARK 620 3 HOH A 245 O 96.2 174.8 REMARK 620 4 HOH A 248 O 94.3 103.7 75.6 REMARK 620 5 HOH A 251 O 88.8 97.7 82.9 158.5 REMARK 620 6 HOH A 262 O 176.8 90.3 84.6 88.9 88.2 REMARK 620 N 1 2 3 4 5 DBREF 7FAO A -1 95 PDB 7FAO 7FAO -1 95 DBREF 7FAO C -1 95 PDB 7FAO 7FAO -1 95 SEQRES 1 A 97 GLY SER HIS MET ASP ILE GLN VAL GLN VAL ASN ILE ASP SEQRES 2 A 97 ASP ASN GLY LYS ASN PHE ASP TYR THR TYR THR VAL THR SEQRES 3 A 97 THR GLU SER GLU LEU GLN LYS VAL LEU ASN GLU LEU MET SEQRES 4 A 97 ASP TYR ILE LYS ALA ALA GLY ALA ALA ARG VAL ARG ILE SEQRES 5 A 97 SER ILE THR ALA ARG THR SER SER GLU ALA GLU LYS PHE SEQRES 6 A 97 ALA ALA ILE LEU ARG LYS VAL PHE ALA GLU LEU GLY TYR SEQRES 7 A 97 ASN ASP ILE ASN VAL THR PHE ASP GLY ASP THR VAL THR SEQRES 8 A 97 VAL GLU GLY GLN LEU GLU SEQRES 1 C 97 GLY SER HIS MET ASP ILE GLN VAL GLN VAL ASN ILE ASP SEQRES 2 C 97 ASP ASN GLY LYS ASN PHE ASP TYR THR TYR THR VAL THR SEQRES 3 C 97 THR GLU SER GLU LEU GLN LYS VAL LEU ASN GLU LEU MET SEQRES 4 C 97 ASP TYR ILE LYS ALA ALA GLY ALA ALA ARG VAL ARG ILE SEQRES 5 C 97 SER ILE THR ALA ARG THR SER SER GLU ALA GLU LYS PHE SEQRES 6 C 97 ALA ALA ILE LEU ARG LYS VAL PHE ALA GLU LEU GLY TYR SEQRES 7 C 97 ASN ASP ILE ASN VAL THR PHE ASP GLY ASP THR VAL THR SEQRES 8 C 97 VAL GLU GLY GLN LEU GLU HET MG A 101 1 HETNAM MG MAGNESIUM ION FORMUL 3 MG MG 2+ FORMUL 4 HOH *127(H2 O) HELIX 1 AA1 THR A 25 GLY A 44 1 20 HELIX 2 AA2 THR A 56 LEU A 74 1 19 HELIX 3 AA3 THR C 25 GLY C 44 1 20 HELIX 4 AA4 THR C 56 GLY C 75 1 20 SHEET 1 AA110 LYS A 15 VAL A 23 0 SHEET 2 AA110 ILE A 4 ASP A 12 -1 N VAL A 6 O TYR A 21 SHEET 3 AA110 ARG A 47 THR A 53 -1 O THR A 53 N GLN A 5 SHEET 4 AA110 THR A 87 GLN A 93 -1 O VAL A 88 N ILE A 52 SHEET 5 AA110 ASP A 78 ASP A 84 -1 N THR A 82 O THR A 89 SHEET 6 AA110 ASP C 78 ASP C 84 -1 O ILE C 79 N ILE A 79 SHEET 7 AA110 THR C 87 GLN C 93 -1 O THR C 89 N THR C 82 SHEET 8 AA110 ARG C 47 THR C 53 -1 N VAL C 48 O GLY C 92 SHEET 9 AA110 ILE C 4 ASP C 12 -1 N ASP C 11 O ARG C 47 SHEET 10 AA110 LYS C 15 VAL C 23 -1 O VAL C 23 N ILE C 4 LINK OE2 GLU A 35 MG MG A 101 1555 1555 2.05 LINK MG MG A 101 O HOH A 213 1555 1555 1.95 LINK MG MG A 101 O HOH A 245 1555 1555 1.88 LINK MG MG A 101 O AHOH A 248 1555 1555 2.01 LINK MG MG A 101 O HOH A 251 1555 1555 2.26 LINK MG MG A 101 O HOH A 262 1555 1555 2.09 CRYST1 24.015 86.298 40.130 90.00 97.18 90.00 P 1 21 1 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 0.041641 0.000000 0.005243 0.00000 SCALE2 0.000000 0.011588 0.000000 0.00000 SCALE3 0.000000 0.000000 0.025116 0.00000