HEADER POLYMERASE BINDING PROTEIN 08-FEB-17 5N35 TITLE GADOLINIUM PHASED PBP2 (SSO6202) AT 2.2 ANG COMPND MOL_ID: 1; COMPND 2 MOLECULE: POLB1 BINDING PROTEIN 2 (PBP2); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SULFOLOBUS SOLFATARICUS; SOURCE 3 ORGANISM_TAXID: 2287; SOURCE 4 GENE: SSOP1_0579, SULA_1676, SULB_1677, SULC_1675; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_VARIANT: ROSETTA KEYWDS POLB1 BINDING PROTEIN 2, ARCHAEAL DNA POLYMERASE HOLOENZYME, PROTEIN KEYWDS 2 BINDING, POLYMERASE BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR J.YAN,T.R.BEATTIE,A.L.ROJAS,K.SCHERMERHORN,T.GRISTWOOD,J.C.TRINIDAD, AUTHOR 2 S.V.ALBERS,P.ROVERSI,A.F.GARDNER,N.G.A.ABRESCIA,S.D.BELL REVDAT 2 06-DEC-17 5N35 1 AUTHOR REVDAT 1 17-MAY-17 5N35 0 JRNL AUTH J.YAN,T.R.BEATTIE,A.L.ROJAS,K.SCHERMERHORN,T.GRISTWOOD, JRNL AUTH 2 J.C.TRINIDAD,S.V.ALBERS,P.ROVERSI,A.F.GARDNER, JRNL AUTH 3 N.G.A.ABRESCIA,S.D.BELL JRNL TITL IDENTIFICATION AND CHARACTERIZATION OF A HETEROTRIMERIC JRNL TITL 2 ARCHAEAL DNA POLYMERASE HOLOENZYME. JRNL REF NAT COMMUN V. 8 15075 2017 JRNL REFN ESSN 2041-1723 JRNL PMID 28462924 JRNL DOI 10.1038/NCOMMS15075 REMARK 2 REMARK 2 RESOLUTION. 2.24 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : BUSTER 2.11.2 REMARK 3 AUTHORS : BRICOGNE,BLANC,BRANDL,FLENSBURG,KELLER, REMARK 3 : PACIOREK,ROVERSI,SHARFF,SMART,VONRHEIN, REMARK 3 : WOMACK,MATTHEWS,TEN EYCK,TRONRUD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.24 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 31.08 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 93.6 REMARK 3 NUMBER OF REFLECTIONS : 3740 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : FREE R-VALUE REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.229 REMARK 3 R VALUE (WORKING SET) : 0.227 REMARK 3 FREE R VALUE : 0.275 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.570 REMARK 3 FREE R VALUE TEST SET COUNT : 171 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 5 REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 2.24 REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 2.50 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 93.62 REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 874 REMARK 3 BIN R VALUE (WORKING + TEST SET) : 0.3776 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 832 REMARK 3 BIN R VALUE (WORKING SET) : 0.3766 REMARK 3 BIN FREE R VALUE : 0.3961 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.81 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 42 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 468 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 24 REMARK 3 SOLVENT ATOMS : 30 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 30.90 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 37.15 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.63420 REMARK 3 B22 (A**2) : -1.63420 REMARK 3 B33 (A**2) : 3.26830 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.401 REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : 0.317 REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : 0.240 REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : 0.304 REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : 0.235 REMARK 3 REMARK 3 REFERENCES: BLOW, D. (2002) ACTA CRYST D58, 792-797 REMARK 3 CRUICKSHANK, D.W.J. (1999) ACTA CRYST D55, 583-601 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.915 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.881 REMARK 3 REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15 REMARK 3 TERM COUNT WEIGHT FUNCTION. REMARK 3 BOND LENGTHS : 521 ; 2.000 ; HARMONIC REMARK 3 BOND ANGLES : 710 ; 2.000 ; HARMONIC REMARK 3 TORSION ANGLES : 195 ; 2.000 ; SINUSOIDAL REMARK 3 TRIGONAL CARBON PLANES : 15 ; 2.000 ; HARMONIC REMARK 3 GENERAL PLANES : 68 ; 5.000 ; HARMONIC REMARK 3 ISOTROPIC THERMAL FACTORS : 521 ; 20.000 ; HARMONIC REMARK 3 BAD NON-BONDED CONTACTS : 0 ; 5.000 ; SEMIHARMONIC REMARK 3 IMPROPER TORSIONS : NULL ; NULL ; NULL REMARK 3 PSEUDOROTATION ANGLES : NULL ; NULL ; NULL REMARK 3 CHIRAL IMPROPER TORSION : 67 ; 5.000 ; SEMIHARMONIC REMARK 3 SUM OF OCCUPANCIES : NULL ; NULL ; NULL REMARK 3 UTILITY DISTANCES : NULL ; NULL ; NULL REMARK 3 UTILITY ANGLES : NULL ; NULL ; NULL REMARK 3 UTILITY TORSION : NULL ; NULL ; NULL REMARK 3 IDEAL-DIST CONTACT TERM : 674 ; 4.000 ; SEMIHARMONIC REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 1.29 REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 2.42 REMARK 3 OTHER TORSION ANGLES (DEGREES) : 19.55 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE REFINEMENT WAS CARRIED OUT WITH THE REMARK 3 DATA FROM REMOTE 1. REMARK 4 REMARK 4 5N35 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 09-FEB-17. REMARK 100 THE DEPOSITION ID IS D_1200001999. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-NOV-12; 22-NOV-12; 22-NOV-16 REMARK 200 TEMPERATURE (KELVIN) : 100; 100; 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y; Y; Y REMARK 200 RADIATION SOURCE : ESRF; ESRF; ESRF REMARK 200 BEAMLINE : ID29; ID29; ID29 REMARK 200 X-RAY GENERATOR MODEL : NULL; NULL; NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M; M; M REMARK 200 WAVELENGTH OR RANGE (A) : 1.71076; 1.71145; 1.70371 REMARK 200 MONOCHROMATOR : NULL; NULL; NULL REMARK 200 OPTICS : NULL; NULL; NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL; PIXEL; PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M; DECTRIS REMARK 200 PILATUS 6M; DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 3963 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 31.100 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 200 DATA REDUNDANCY : 17.00 REMARK 200 R MERGE (I) : 0.06000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 31.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : 90.7 REMARK 200 DATA REDUNDANCY IN SHELL : 8.70 REMARK 200 R MERGE FOR SHELL (I) : 0.07000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD; MAD; MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: SHARP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.28 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.29 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PROTEIN: 42.7 MG/ML IN 20 MM HEPES PH REMARK 280 7.5, 0.3 M NACL, 1MM MGCL2 AND 1MM B-ME. CRYSTALLIZATION BUFFER: REMARK 280 0.2 M NANO3, 20% PEG 3350, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 294.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 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+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 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 23.78667 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 11.89333 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 11.89333 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 23.78667 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1070 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 3940 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -15.0 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 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 9 REMARK 465 SER A 10 REMARK 465 LYS A 71 REMARK 465 SER A 72 REMARK 465 THR A 73 REMARK 465 ASP A 74 REMARK 465 LYS A 75 REMARK 465 LYS A 76 REMARK 465 LEU A 77 REMARK 465 GLU A 78 REMARK 465 HIS A 79 REMARK 465 HIS A 80 REMARK 465 HIS A 81 REMARK 465 HIS A 82 REMARK 465 HIS A 83 REMARK 465 HIS A 84 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GD A 100 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GD A 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 102 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NO3 A 103 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 104 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 105 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5N41 RELATED DB: PDB REMARK 900 NATIVE STRUCTURE AT 1.35 ANG DBREF1 5N35 A 9 76 UNP A0A0E3GTJ4_SULSF DBREF2 5N35 A A0A0E3GTJ4 9 76 SEQADV 5N35 LEU A 77 UNP A0A0E3GTJ EXPRESSION TAG SEQADV 5N35 GLU A 78 UNP A0A0E3GTJ EXPRESSION TAG SEQADV 5N35 HIS A 79 UNP A0A0E3GTJ EXPRESSION TAG SEQADV 5N35 HIS A 80 UNP A0A0E3GTJ EXPRESSION TAG SEQADV 5N35 HIS A 81 UNP A0A0E3GTJ EXPRESSION TAG SEQADV 5N35 HIS A 82 UNP A0A0E3GTJ EXPRESSION TAG SEQADV 5N35 HIS A 83 UNP A0A0E3GTJ EXPRESSION TAG SEQADV 5N35 HIS A 84 UNP A0A0E3GTJ EXPRESSION TAG SEQRES 1 A 76 MET SER VAL ASN GLN LYS GLU ILE GLU ILE ALA ILE GLU SEQRES 2 A 76 TYR PHE LYS ASN TYR ILE SER VAL GLY GLU ILE VAL ALA SEQRES 3 A 76 THR MET ASP LEU LYS ALA ARG GLY ILE SER ASN PRO GLN SEQRES 4 A 76 ALA VAL ILE SER LYS LEU ILE GLU MET GLY ILE ILE GLU SEQRES 5 A 76 LYS GLY GLU GLY CYS TYR ASN LEU VAL ARG LYS SER THR SEQRES 6 A 76 ASP LYS LYS LEU GLU HIS HIS HIS HIS HIS HIS HET GD A 100 1 HET GD A 101 1 HET GOL A 102 14 HET NO3 A 103 4 HET GOL A 104 14 HET GOL A 105 14 HETNAM GD GADOLINIUM ATOM HETNAM GOL GLYCEROL HETNAM NO3 NITRATE ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 GD 2(GD) FORMUL 4 GOL 3(C3 H8 O3) FORMUL 5 NO3 N O3 1- FORMUL 8 HOH *30(H2 O) HELIX 1 AA1 ASN A 12 TYR A 26 1 15 HELIX 2 AA2 GLU A 31 ARG A 41 1 11 HELIX 3 AA3 ASN A 45 MET A 56 1 12 SHEET 1 AA1 3 SER A 28 GLY A 30 0 SHEET 2 AA1 3 CYS A 65 LEU A 68 -1 O TYR A 66 N VAL A 29 SHEET 3 AA1 3 ILE A 59 LYS A 61 -1 N GLU A 60 O ASN A 67 SSBOND 1 CYS A 65 CYS A 65 1555 5676 2.04 LINK OE1 GLU A 60 GD GD A 100 1555 1555 2.26 LINK O LYS A 61 GD GD A 101 1555 1555 2.62 SITE 1 AC1 1 GLU A 60 SITE 1 AC2 2 LYS A 61 GLY A 62 SITE 1 AC3 5 GLY A 30 GLU A 31 ILE A 32 VAL A 33 SITE 2 AC3 5 GLY A 64 SITE 1 AC4 5 ILE A 20 LYS A 24 ASP A 37 ARG A 41 SITE 2 AC4 5 ILE A 58 SITE 1 AC5 4 LYS A 61 GLY A 62 GLU A 63 GLY A 64 SITE 1 AC6 4 ASN A 45 GLN A 47 ALA A 48 SER A 51 CRYST1 62.150 62.150 35.680 90.00 90.00 120.00 P 32 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 0.016090 0.009290 0.000000 0.00000 SCALE2 0.000000 0.018579 0.000000 0.00000 SCALE3 0.000000 0.000000 0.028027 0.00000