HEADER REPLICATION/DNA 01-APR-20 6WDZ TITLE PORCINE CIRCOVIRUS 2 REP DOMAIN COMPLEXED WITH A SINGLE-STRANDED DNA TITLE 2 10-MER COMPRISING THE CLEAVAGE SITE COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*TP*AP*GP*TP*AP*TP*TP*AP*CP*C)-3'); COMPND 3 CHAIN: C, I, F, J; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: ATP-DEPENDENT HELICASE REP; COMPND 7 CHAIN: D, G, A; COMPND 8 SYNONYM: REPP,REPLICATION-ASSOCIATED PROTEIN; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: PORCINE CIRCOVIRUS 2; SOURCE 4 ORGANISM_TAXID: 85708; SOURCE 5 MOL_ID: 2; SOURCE 6 ORGANISM_SCIENTIFIC: PORCINE CIRCOVIRUS 2; SOURCE 7 ORGANISM_COMMON: PCV2; SOURCE 8 ORGANISM_TAXID: 85708; SOURCE 9 GENE: REP; SOURCE 10 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 11 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS HUH-TAG, HUH MOTIF, REP DOMAIN, VIRAL PROTEIN, SINGLE STRANDED DNA, KEYWDS 2 SSDNA, SSDNA BINDING, REPLICATION, DNA BINDING PROTEIN, REPLICATION- KEYWDS 3 DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR L.A.LITZAU,K.TOMPKINS,K.SHI,A.NELSON,R.L.EVANS III,W.R.GORDON REVDAT 3 18-OCT-23 6WDZ 1 REMARK REVDAT 2 17-MAR-21 6WDZ 1 JRNL REVDAT 1 16-DEC-20 6WDZ 0 JRNL AUTH K.J.TOMPKINS,M.HOUTTI,L.A.LITZAU,E.J.AIRD,B.A.EVERETT, JRNL AUTH 2 A.T.NELSON,L.PORNSCHLOEGL,L.K.LIMON-SWANSON,R.L.EVANS, JRNL AUTH 3 K.EVANS,K.SHI,H.AIHARA,W.R.GORDON JRNL TITL MOLECULAR UNDERPINNINGS OF SSDNA SPECIFICITY BY REP JRNL TITL 2 HUH-ENDONUCLEASES AND IMPLICATIONS FOR HUH-TAG MULTIPLEXING JRNL TITL 3 AND ENGINEERING. JRNL REF NUCLEIC ACIDS RES. V. 49 1046 2021 JRNL REFN ESSN 1362-4962 JRNL PMID 33410911 JRNL DOI 10.1093/NAR/GKAA1248 REMARK 2 REMARK 2 RESOLUTION. 2.03 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.18.2_3874 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) : 2.03 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.10 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 93.0 REMARK 3 NUMBER OF REFLECTIONS : 26261 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.232 REMARK 3 R VALUE (WORKING SET) : 0.229 REMARK 3 FREE R VALUE : 0.280 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.710 REMARK 3 FREE R VALUE TEST SET COUNT : 2323 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 43.1000 - 5.2200 0.89 2595 174 0.2275 0.2600 REMARK 3 2 5.2200 - 4.1400 0.96 2827 137 0.1980 0.2279 REMARK 3 3 4.1400 - 3.6200 0.96 2851 163 0.1876 0.2144 REMARK 3 4 3.6200 - 3.2900 0.97 2878 120 0.1896 0.2778 REMARK 3 5 3.2900 - 3.0500 0.87 2576 121 0.2186 0.2701 REMARK 3 6 3.0500 - 2.8700 0.93 2738 146 0.2508 0.2870 REMARK 3 7 2.8700 - 2.7300 0.95 2803 126 0.2559 0.3669 REMARK 3 8 2.7300 - 2.6100 0.95 2802 169 0.2466 0.3243 REMARK 3 9 2.6100 - 2.5100 0.96 2835 133 0.2661 0.2889 REMARK 3 10 2.5100 - 2.4200 0.95 2819 118 0.2756 0.4072 REMARK 3 11 2.4200 - 2.3500 0.96 2901 129 0.2476 0.3958 REMARK 3 12 2.3500 - 2.2800 0.95 2771 160 0.2656 0.3040 REMARK 3 13 2.2800 - 2.2200 0.93 2666 174 0.2717 0.3134 REMARK 3 14 2.2200 - 2.1700 0.86 2576 106 0.2691 0.3023 REMARK 3 15 2.1700 - 2.1200 0.92 2750 125 0.2541 0.3357 REMARK 3 16 2.1200 - 2.0700 0.93 2753 122 0.2714 0.2998 REMARK 3 17 2.0700 - 2.0300 0.94 2814 100 0.2725 0.2905 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) : 0.290 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 31.820 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 25.87 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 32.54 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL 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 6WDZ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 02-APR-20. REMARK 100 THE DEPOSITION ID IS D_1000247975. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-MAR-20 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 : APS REMARK 200 BEAMLINE : 24-ID-C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : .97910 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 S 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 26261 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.030 REMARK 200 RESOLUTION RANGE LOW (A) : 43.100 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.5 REMARK 200 DATA REDUNDANCY : 2.900 REMARK 200 R MERGE (I) : 0.06745 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.4900 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.03 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.10 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.2 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.36190 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.630 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: 5XOR + MODELED 10-MER REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.59 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.14 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M AMMONIUM ACETATE, 25% REMARK 280 POLYETHYLENE GLYCOL 3,350, 0.1M BIS-TRIS PH 7 SOAKED IN 25% REMARK 280 GLYCEROL FOR CRYOPROTECTANT, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 64 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 -X,-Y,Z REMARK 290 5555 Y,-X+Y,Z+1/3 REMARK 290 6555 X-Y,X,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 24.56500 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 49.13000 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 24.56500 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 49.13000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3, 4 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: 2040 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6260 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -6.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2020 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6410 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -8.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: D, F 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: 3 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: 2400 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6350 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -3.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: I, G 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: 4 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: 1260 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: J 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 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 I 404 LIES ON A SPECIAL POSITION. REMARK 375 HOH G 327 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 PRO D 2 REMARK 465 SER D 3 REMARK 465 LYS D 4 REMARK 465 LYS D 5 REMARK 465 ASN D 6 REMARK 465 GLY D 7 REMARK 465 ARG D 8 REMARK 465 SER D 9 REMARK 465 GLY D 10 REMARK 465 GLN D 113 REMARK 465 GLY D 114 REMARK 465 GLN D 115 REMARK 465 ARG D 116 REMARK 465 PRO G 2 REMARK 465 SER G 3 REMARK 465 LYS G 4 REMARK 465 LYS G 5 REMARK 465 ASN G 6 REMARK 465 GLY G 7 REMARK 465 ARG G 8 REMARK 465 SER G 9 REMARK 465 GLY G 10 REMARK 465 PRO G 11 REMARK 465 ASN G 50 REMARK 465 GLU G 51 REMARK 465 GLN G 113 REMARK 465 GLY G 114 REMARK 465 GLN G 115 REMARK 465 ARG G 116 REMARK 465 DT J 299 REMARK 465 DA J 300 REMARK 465 DG J 301 REMARK 465 DT J 302 REMARK 465 DA J 303 REMARK 465 DT J 304 REMARK 465 PRO A 2 REMARK 465 SER A 3 REMARK 465 LYS A 4 REMARK 465 LYS A 5 REMARK 465 ASN A 6 REMARK 465 GLY A 7 REMARK 465 ARG A 8 REMARK 465 SER A 9 REMARK 465 GLY A 10 REMARK 465 PRO A 11 REMARK 465 GLN A 113 REMARK 465 GLY A 114 REMARK 465 GLN A 115 REMARK 465 ARG A 116 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 GLU D 26 CG CD OE1 OE2 REMARK 470 GLU D 51 CG CD OE1 OE2 REMARK 470 ASN G 71 CG OD1 ND2 REMARK 470 LYS G 85 CG CD CE NZ REMARK 470 LYS G 87 CG CD CE NZ REMARK 470 GLU A 51 CG CD OE1 OE2 REMARK 470 GLU A 52 CG CD OE1 OE2 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 LYS D 30 CG REMARK 480 LYS D 31 NZ REMARK 480 ARG D 33 NE CZ REMARK 480 GLU D 52 CD REMARK 480 ASP G 27 CG REMARK 480 HIS A 14 CE1 REMARK 480 ASP A 27 CG REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH A 344 O HOH A 352 2.03 REMARK 500 O CYS G 107 O HOH G 301 2.08 REMARK 500 OE1 GLN D 12 O HOH D 301 2.11 REMARK 500 O HOH D 336 O HOH D 339 2.13 REMARK 500 O HOH D 310 O HOH F 402 2.14 REMARK 500 O HOH D 305 O HOH D 308 2.14 REMARK 500 O HOH G 316 O HOH G 329 2.16 REMARK 500 O HOH F 403 O HOH F 406 2.17 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 DC J 308 O3' DC J 308 C3' -0.057 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 DT C 302 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 DA C 306 O4' - C1' - N9 ANGL. DEV. = 4.3 DEGREES REMARK 500 DT I 302 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 DA I 306 O4' - C1' - N9 ANGL. DEV. = 3.4 DEGREES REMARK 500 DC I 307 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 DT F 302 O4' - C1' - N1 ANGL. DEV. = 3.3 DEGREES REMARK 500 DA F 306 O4' - C1' - N9 ANGL. DEV. = 3.9 DEGREES REMARK 500 ARG A 54 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 REMARK 500 REMARK: NULL 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 A 102 83.69 -154.02 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 362 DISTANCE = 6.35 ANGSTROMS 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 MN A 201 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DT C 305 O3' REMARK 620 2 DA C 306 OP1 64.2 REMARK 620 3 GLU A 48 OE1 157.3 93.2 REMARK 620 4 HIS A 57 NE2 94.2 157.9 108.5 REMARK 620 5 GLN A 59 OE1 84.0 82.8 95.5 90.7 REMARK 620 6 HOH A 339 O 83.4 91.7 96.1 90.3 167.4 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN D 201 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU D 48 OE1 REMARK 620 2 HIS D 57 NE2 93.0 REMARK 620 3 GLN D 59 OE1 101.3 86.2 REMARK 620 4 HOH D 302 O 72.7 95.5 173.8 REMARK 620 5 DT F 305 O3' 158.8 102.1 94.6 90.8 REMARK 620 6 DA F 306 OP1 103.5 163.5 91.0 88.9 61.9 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN G 203 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DT I 305 O3' REMARK 620 2 DA I 306 OP1 57.8 REMARK 620 3 GLU G 48 OE1 144.7 88.6 REMARK 620 4 HIS G 57 NE2 102.1 159.0 112.3 REMARK 620 5 GLN G 59 OE1 76.6 69.8 103.4 101.4 REMARK 620 6 HOH G 315 O 83.9 86.7 83.7 97.7 155.1 REMARK 620 N 1 2 3 4 5 DBREF 6WDZ C 299 308 PDB 6WDZ 6WDZ 299 308 DBREF1 6WDZ D 2 116 UNP A0A060L113_PCV2 DBREF2 6WDZ D A0A060L113 2 116 DBREF 6WDZ I 299 308 PDB 6WDZ 6WDZ 299 308 DBREF1 6WDZ G 2 116 UNP A0A060L113_PCV2 DBREF2 6WDZ G A0A060L113 2 116 DBREF 6WDZ F 299 308 PDB 6WDZ 6WDZ 299 308 DBREF 6WDZ J 299 308 PDB 6WDZ 6WDZ 299 308 DBREF1 6WDZ A 2 116 UNP A0A060L113_PCV2 DBREF2 6WDZ A A0A060L113 2 116 SEQADV 6WDZ PHE D 96 UNP A0A060L11 TYR 96 CONFLICT SEQADV 6WDZ PHE G 96 UNP A0A060L11 TYR 96 CONFLICT SEQADV 6WDZ PHE A 96 UNP A0A060L11 TYR 96 CONFLICT SEQRES 1 C 10 DT DA DG DT DA DT DT DA DC DC SEQRES 1 D 115 PRO SER LYS LYS ASN GLY ARG SER GLY PRO GLN PRO HIS SEQRES 2 D 115 LYS ARG TRP VAL PHE THR LEU ASN ASN PRO SER GLU ASP SEQRES 3 D 115 GLU ARG LYS LYS ILE ARG ASP LEU PRO ILE SER LEU PHE SEQRES 4 D 115 ASP TYR PHE ILE VAL GLY GLU GLU GLY ASN GLU GLU GLY SEQRES 5 D 115 ARG THR PRO HIS LEU GLN GLY PHE ALA ASN PHE VAL LYS SEQRES 6 D 115 LYS GLN THR PHE ASN LYS VAL LYS TRP TYR LEU GLY ALA SEQRES 7 D 115 ARG CYS HIS ILE GLU LYS ALA LYS GLY THR ASP GLN GLN SEQRES 8 D 115 ASN LYS GLU PHE CYS SER LYS GLU GLY ASN LEU LEU MET SEQRES 9 D 115 GLU CYS GLY ALA PRO ARG SER GLN GLY GLN ARG SEQRES 1 I 10 DT DA DG DT DA DT DT DA DC DC SEQRES 1 G 115 PRO SER LYS LYS ASN GLY ARG SER GLY PRO GLN PRO HIS SEQRES 2 G 115 LYS ARG TRP VAL PHE THR LEU ASN ASN PRO SER GLU ASP SEQRES 3 G 115 GLU ARG LYS LYS ILE ARG ASP LEU PRO ILE SER LEU PHE SEQRES 4 G 115 ASP TYR PHE ILE VAL GLY GLU GLU GLY ASN GLU GLU GLY SEQRES 5 G 115 ARG THR PRO HIS LEU GLN GLY PHE ALA ASN PHE VAL LYS SEQRES 6 G 115 LYS GLN THR PHE ASN LYS VAL LYS TRP TYR LEU GLY ALA SEQRES 7 G 115 ARG CYS HIS ILE GLU LYS ALA LYS GLY THR ASP GLN GLN SEQRES 8 G 115 ASN LYS GLU PHE CYS SER LYS GLU GLY ASN LEU LEU MET SEQRES 9 G 115 GLU CYS GLY ALA PRO ARG SER GLN GLY GLN ARG SEQRES 1 F 10 DT DA DG DT DA DT DT DA DC DC SEQRES 1 J 10 DT DA DG DT DA DT DT DA DC DC SEQRES 1 A 115 PRO SER LYS LYS ASN GLY ARG SER GLY PRO GLN PRO HIS SEQRES 2 A 115 LYS ARG TRP VAL PHE THR LEU ASN ASN PRO SER GLU ASP SEQRES 3 A 115 GLU ARG LYS LYS ILE ARG ASP LEU PRO ILE SER LEU PHE SEQRES 4 A 115 ASP TYR PHE ILE VAL GLY GLU GLU GLY ASN GLU GLU GLY SEQRES 5 A 115 ARG THR PRO HIS LEU GLN GLY PHE ALA ASN PHE VAL LYS SEQRES 6 A 115 LYS GLN THR PHE ASN LYS VAL LYS TRP TYR LEU GLY ALA SEQRES 7 A 115 ARG CYS HIS ILE GLU LYS ALA LYS GLY THR ASP GLN GLN SEQRES 8 A 115 ASN LYS GLU PHE CYS SER LYS GLU GLY ASN LEU LEU MET SEQRES 9 A 115 GLU CYS GLY ALA PRO ARG SER GLN GLY GLN ARG HET MN D 201 1 HET EDO G 201 4 HET EDO G 202 4 HET MN G 203 1 HET MN A 201 1 HETNAM MN MANGANESE (II) ION HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 8 MN 3(MN 2+) FORMUL 9 EDO 2(C2 H6 O2) FORMUL 13 HOH *194(H2 O) HELIX 1 AA1 SER D 25 ASP D 34 1 10 HELIX 2 AA2 PRO D 36 SER D 38 5 3 HELIX 3 AA3 THR D 69 GLY D 78 1 10 HELIX 4 AA4 THR D 89 LYS D 99 1 11 HELIX 5 AA5 SER G 25 ARG G 33 1 9 HELIX 6 AA6 PRO G 36 SER G 38 5 3 HELIX 7 AA7 THR G 69 GLY G 78 1 10 HELIX 8 AA8 THR G 89 SER G 98 1 10 HELIX 9 AA9 SER A 25 ASP A 34 1 10 HELIX 10 AB1 PRO A 36 SER A 38 5 3 HELIX 11 AB2 THR A 69 GLY A 78 1 10 HELIX 12 AB3 THR A 89 LYS A 99 1 11 SHEET 1 AA1 5 HIS D 82 LYS D 85 0 SHEET 2 AA1 5 HIS D 14 ASN D 22 -1 N THR D 20 O HIS D 82 SHEET 3 AA1 5 HIS D 57 GLN D 68 -1 O ALA D 62 N TRP D 17 SHEET 4 AA1 5 PHE D 40 GLU D 48 -1 N ASP D 41 O ASN D 63 SHEET 5 AA1 5 LEU D 103 GLY D 108 -1 O LEU D 104 N VAL D 45 SHEET 1 AA2 5 HIS G 82 LYS G 85 0 SHEET 2 AA2 5 HIS G 14 ASN G 22 -1 N VAL G 18 O GLU G 84 SHEET 3 AA2 5 HIS G 57 GLN G 68 -1 O GLN G 68 N HIS G 14 SHEET 4 AA2 5 PHE G 40 GLU G 48 -1 N ASP G 41 O ASN G 63 SHEET 5 AA2 5 LEU G 103 GLY G 108 -1 O LEU G 104 N VAL G 45 SHEET 1 AA3 5 HIS A 82 LYS A 85 0 SHEET 2 AA3 5 HIS A 14 ASN A 22 -1 N THR A 20 O HIS A 82 SHEET 3 AA3 5 HIS A 57 GLN A 68 -1 O ALA A 62 N TRP A 17 SHEET 4 AA3 5 PHE A 40 GLU A 48 -1 N TYR A 42 O ASN A 63 SHEET 5 AA3 5 LEU A 103 GLY A 108 -1 O LEU A 104 N VAL A 45 LINK O3' DT C 305 MN MN A 201 1555 1555 2.34 LINK OP1 DA C 306 MN MN A 201 1555 1555 2.17 LINK OE1 GLU D 48 MN MN D 201 1555 1555 1.78 LINK NE2 HIS D 57 MN MN D 201 1555 1555 2.15 LINK OE1 GLN D 59 MN MN D 201 1555 1555 2.17 LINK MN MN D 201 O HOH D 302 1555 1555 2.00 LINK MN MN D 201 O3' DT F 305 1555 1555 2.48 LINK MN MN D 201 OP1 DA F 306 1555 1555 2.22 LINK O3' DT I 305 MN MN G 203 1555 1555 2.60 LINK OP1 DA I 306 MN MN G 203 1555 1555 2.53 LINK OE1 GLU G 48 MN MN G 203 1555 1555 1.91 LINK NE2 HIS G 57 MN MN G 203 1555 1555 2.04 LINK OE1 GLN G 59 MN MN G 203 1555 1555 2.59 LINK MN MN G 203 O HOH G 315 1555 1555 2.20 LINK OE1 GLU A 48 MN MN A 201 1555 1555 2.01 LINK NE2 HIS A 57 MN MN A 201 1555 1555 2.26 LINK OE1 GLN A 59 MN MN A 201 1555 1555 2.05 LINK MN MN A 201 O HOH A 339 1555 1555 2.20 CRYST1 99.527 99.527 73.695 90.00 90.00 120.00 P 64 24 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 0.010048 0.005801 0.000000 0.00000 SCALE2 0.000000 0.011602 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013569 0.00000