HEADER DNA BINDING PROTEIN 26-APR-19 6JYK TITLE CRYSTAL STRUCTURE OF C. CRESCENTUS FREE GAPR COMPND MOL_ID: 1; COMPND 2 MOLECULE: UPF0335 PROTEIN CCNA_03428; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: GAPR (GROWTH-ASSOCIATED A/T-BINDING PROTEIN INVOLVED IN COMPND 5 REGULATION); COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CAULOBACTER VIBRIOIDES (STRAIN NA1000 / CB15N); SOURCE 3 ORGANISM_TAXID: 565050; SOURCE 4 STRAIN: NA1000 / CB15N; SOURCE 5 GENE: CCNA_03428; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS C. CRESCENTUS, FREE, NAPS, DNA BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR B.XIA,Q.HUANG REVDAT 4 22-NOV-23 6JYK 1 REMARK REVDAT 3 07-OCT-20 6JYK 1 JRNL REVDAT 2 19-AUG-20 6JYK 1 JRNL REVDAT 1 05-AUG-20 6JYK 0 JRNL AUTH Q.HUANG,B.DUAN,X.DONG,S.FAN,B.XIA JRNL TITL GAPR BINDS DNA THROUGH DYNAMIC OPENING OF ITS TETRAMERIC JRNL TITL 2 INTERFACE. JRNL REF NUCLEIC ACIDS RES. V. 48 9372 2020 JRNL REFN ESSN 1362-4962 JRNL PMID 32756896 JRNL DOI 10.1093/NAR/GKAA644 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.9_1692 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.78 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 3 NUMBER OF REFLECTIONS : 13439 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.204 REMARK 3 R VALUE (WORKING SET) : 0.203 REMARK 3 FREE R VALUE : 0.212 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.020 REMARK 3 FREE R VALUE TEST SET COUNT : 1347 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 43.7867 - 4.3079 0.97 1292 144 0.2046 0.1967 REMARK 3 2 4.3079 - 3.4197 0.96 1206 142 0.1896 0.1974 REMARK 3 3 3.4197 - 2.9875 0.97 1209 133 0.2024 0.2176 REMARK 3 4 2.9875 - 2.7144 0.99 1214 141 0.2056 0.2084 REMARK 3 5 2.7144 - 2.5199 0.99 1198 134 0.1998 0.2414 REMARK 3 6 2.5199 - 2.3713 1.00 1231 132 0.1994 0.2387 REMARK 3 7 2.3713 - 2.2526 0.99 1190 136 0.1987 0.2056 REMARK 3 8 2.2526 - 2.1545 0.95 1166 127 0.2260 0.2060 REMARK 3 9 2.1545 - 2.0716 1.00 1210 130 0.2147 0.2664 REMARK 3 10 2.0716 - 2.0001 0.98 1176 128 0.2630 0.2983 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) : 0.210 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.120 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 : 0.009 617 REMARK 3 ANGLE : 0.891 822 REMARK 3 CHIRALITY : 0.037 95 REMARK 3 PLANARITY : 0.003 106 REMARK 3 DIHEDRAL : 13.029 249 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): -14.4973 4.6437 -15.1884 REMARK 3 T TENSOR REMARK 3 T11: 0.1667 T22: 0.2474 REMARK 3 T33: 0.2784 T12: -0.0190 REMARK 3 T13: 0.0017 T23: -0.0269 REMARK 3 L TENSOR REMARK 3 L11: 0.6047 L22: 1.0604 REMARK 3 L33: 1.7185 L12: -0.2029 REMARK 3 L13: 0.0288 L23: -0.5549 REMARK 3 S TENSOR REMARK 3 S11: 0.0964 S12: -0.0152 S13: 0.0823 REMARK 3 S21: 0.0536 S22: 0.0160 S23: -0.0403 REMARK 3 S31: -0.0677 S32: 0.0310 S33: -0.0935 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 6JYK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 09-MAY-19. REMARK 100 THE DEPOSITION ID IS D_1300011876. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-APR-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.6-8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL17U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9786 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 : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13439 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 43.800 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 200 DATA REDUNDANCY : 5.600 REMARK 200 R MERGE (I) : 0.07300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 37.7000 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) : 2.03 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.54000 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: 6K2J REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 71.59 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.33 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.01M MANGANESE (II) CHLORIDE REMARK 280 TETRAHYDRATE, 0.1M SODIUM CITRATE (PH 5.6), 2.5M 1,6-HEXANEDIOL REMARK 280 AND 0.3% V/V DIMETHYL SULFOXIDE, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 289K 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 36.99967 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 73.99933 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 73.99933 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 36.99967 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: 2710 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11810 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -20.0 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 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 -36.99967 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 HOH A 111 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 124 LIES ON A SPECIAL POSITION. 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 ALA A 2 REMARK 465 ASP A 3 REMARK 465 ASP A 4 REMARK 465 ALA A 5 REMARK 465 ILE A 6 REMARK 465 PRO A 7 REMARK 465 HIS A 8 REMARK 465 THR A 9 REMARK 465 ASP A 10 REMARK 465 GLU A 88 REMARK 465 ILE A 89 REMARK 465 LEU A 90 REMARK 465 GLU A 91 REMARK 465 HIS A 92 REMARK 465 HIS A 93 REMARK 465 HIS A 94 REMARK 465 HIS A 95 REMARK 465 HIS A 96 REMARK 465 HIS A 97 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 VAL A 11 CG1 CG2 DBREF 6JYK A 1 89 UNP B8H4R9 Y3428_CAUVN 1 89 SEQADV 6JYK LEU A 90 UNP B8H4R9 EXPRESSION TAG SEQADV 6JYK GLU A 91 UNP B8H4R9 EXPRESSION TAG SEQADV 6JYK HIS A 92 UNP B8H4R9 EXPRESSION TAG SEQADV 6JYK HIS A 93 UNP B8H4R9 EXPRESSION TAG SEQADV 6JYK HIS A 94 UNP B8H4R9 EXPRESSION TAG SEQADV 6JYK HIS A 95 UNP B8H4R9 EXPRESSION TAG SEQADV 6JYK HIS A 96 UNP B8H4R9 EXPRESSION TAG SEQADV 6JYK HIS A 97 UNP B8H4R9 EXPRESSION TAG SEQRES 1 A 97 MET ALA ASP ASP ALA ILE PRO HIS THR ASP VAL LEU ASN SEQRES 2 A 97 SER THR ALA GLN GLY GLN LEU LYS SER ILE ILE GLU ARG SEQRES 3 A 97 VAL GLU ARG LEU GLU VAL GLU LYS ALA GLU ILE MET GLU SEQRES 4 A 97 GLN ILE LYS GLU VAL TYR ALA GLU ALA LYS GLY ASN GLY SEQRES 5 A 97 PHE ASP VAL LYS VAL LEU LYS LYS VAL VAL ARG ILE ARG SEQRES 6 A 97 LYS GLN ASP ARG ALA LYS ARG GLN GLU GLU ASP ALA ILE SEQRES 7 A 97 LEU ASP LEU TYR LEU SER ALA ILE GLY GLU ILE LEU GLU SEQRES 8 A 97 HIS HIS HIS HIS HIS HIS FORMUL 2 HOH *82(H2 O) HELIX 1 AA1 ASN A 13 ASN A 51 1 39 HELIX 2 AA2 ASP A 54 GLY A 87 1 34 CRYST1 55.007 55.007 110.999 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 0.018180 0.010496 0.000000 0.00000 SCALE2 0.000000 0.020992 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009009 0.00000