HEADER CHAPERONE 11-NOV-20 7DG9 TITLE DPBB DOMAIN OF VCP-LIKE ATPASE FROM AEROPYRUM PERNIX COMPND MOL_ID: 1; COMPND 2 MOLECULE: CELL DIVISION CONTROL PROTEIN 48, AAA FAMILY; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: DPBB DOMAIN; COMPND 5 SYNONYM: VCP-LIKE ATPASE; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: AEROPYRUM PERNIX (STRAIN ATCC 700893 / DSM SOURCE 3 11879 / JCM 9820 / NBRC 100138 / K1); SOURCE 4 ORGANISM_TAXID: 272557; SOURCE 5 GENE: APE_1367; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS DOUBLE PSI BETA BARREL, CHAPERONE EXPDTA X-RAY DIFFRACTION AUTHOR S.YAGI,S.TAGAMI REVDAT 2 17-NOV-21 7DG9 1 JRNL REVDAT 1 29-SEP-21 7DG9 0 JRNL AUTH S.YAGI,A.K.PADHI,J.VUCINIC,S.BARBE,T.SCHIEX,R.NAKAGAWA, JRNL AUTH 2 D.SIMONCINI,K.Y.J.ZHANG,S.TAGAMI JRNL TITL SEVEN AMINO ACID TYPES SUFFICE TO CREATE THE CORE FOLD OF JRNL TITL 2 RNA POLYMERASE. JRNL REF J.AM.CHEM.SOC. V. 143 15998 2021 JRNL REFN ESSN 1520-5126 JRNL PMID 34559526 JRNL DOI 10.1021/JACS.1C05367 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH S.YAGI,A.K.PADHI,J.VUCINIC,S.BARBE,T.SCHIEX,R.NAKAGAWA, REMARK 1 AUTH 2 D.SIMONCINI,K.Y.J.ZHANG,S.TAGAMI REMARK 1 TITL SEVEN AMINO ACID TYPES SUFFICE TO RECONSTRUCT THE CORE FOLD REMARK 1 TITL 2 OF RNA POLYMERASE REMARK 1 REF BIORXIV 2021 REMARK 1 REFN REMARK 1 DOI 10.1101/2021.02.22.432383 REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.14_3260 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) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.08 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 3 NUMBER OF REFLECTIONS : 19198 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.173 REMARK 3 R VALUE (WORKING SET) : 0.169 REMARK 3 FREE R VALUE : 0.207 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.010 REMARK 3 FREE R VALUE TEST SET COUNT : 1922 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 47.0780 - 3.8595 0.86 1080 115 0.1799 0.2143 REMARK 3 2 3.8595 - 3.0636 0.98 1224 138 0.1586 0.1749 REMARK 3 3 3.0636 - 2.6764 1.00 1249 137 0.1754 0.1969 REMARK 3 4 2.6764 - 2.4317 1.00 1241 142 0.1680 0.2074 REMARK 3 5 2.4317 - 2.2574 1.00 1243 138 0.1662 0.2647 REMARK 3 6 2.2574 - 2.1243 1.00 1256 142 0.1596 0.2128 REMARK 3 7 2.1243 - 2.0179 1.00 1239 139 0.1617 0.1874 REMARK 3 8 2.0179 - 1.9301 1.00 1237 138 0.1692 0.2309 REMARK 3 9 1.9301 - 1.8558 1.00 1257 133 0.1688 0.2100 REMARK 3 10 1.8558 - 1.7917 1.00 1282 147 0.1735 0.2262 REMARK 3 11 1.7917 - 1.7357 1.00 1194 133 0.1702 0.1962 REMARK 3 12 1.7357 - 1.6861 1.00 1268 141 0.1700 0.1698 REMARK 3 13 1.6861 - 1.6417 1.00 1250 139 0.1748 0.2337 REMARK 3 14 1.6417 - 1.6020 1.00 1256 140 0.1868 0.2120 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) : 0.140 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.300 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 14.97 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 7DG9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 18-NOV-20. REMARK 100 THE DEPOSITION ID IS D_1300019340. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 31-OCT-19 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 : SPRING-8 REMARK 200 BEAMLINE : BL26B2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX225-HS REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19200 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 200 DATA REDUNDANCY : 7.210 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 33.4100 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.70 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL 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: SAD REMARK 200 SOFTWARE USED: AUTOSOL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 34.79 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.89 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100MM SODIUM ACETATE PH4.5, 20% PEG REMARK 280 1000, 200MM ZINC ACETATE, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-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 13.02000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 47.07800 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 15.53300 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 47.07800 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 13.02000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 15.53300 REMARK 290 SMTRY3 4 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 200 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 5340 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -56.0 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 GLY A 1 REMARK 465 PRO A 2 REMARK 465 GLU A 93 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 224 O HOH A 302 1.51 REMARK 500 O HOH A 209 O HOH A 268 1.74 REMARK 500 O HOH A 286 O HOH A 319 1.96 REMARK 500 NZ LYS A 23 O HOH A 201 1.99 REMARK 500 OE2 GLU A 90 O HOH A 202 2.13 REMARK 500 O HOH A 308 O HOH A 311 2.14 REMARK 500 O HOH A 213 O HOH A 240 2.15 REMARK 500 O HOH A 261 O HOH A 312 2.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 270 O HOH A 334 4556 2.03 REMARK 500 O HOH A 231 O HOH A 298 1655 2.17 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 104 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 85 OD1 REMARK 620 2 HOH A 235 O 89.5 REMARK 620 3 HOH A 296 O 93.4 173.1 REMARK 620 4 HOH A 299 O 176.7 93.8 83.4 REMARK 620 5 HOH A 310 O 102.6 91.0 82.3 78.1 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 105 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 85 OD2 REMARK 620 2 HOH A 335 O 139.5 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 101 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 90 OE2 REMARK 620 2 HOH A 229 O 76.5 REMARK 620 3 HOH A 233 O 78.2 9.5 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 103 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 243 O REMARK 620 2 HOH A 316 O 108.7 REMARK 620 3 HOH A 330 O 90.8 64.6 REMARK 620 N 1 2 DBREF 7DG9 A 3 93 UNP Q9YC86 Q9YC86_AERPE 1 91 SEQADV 7DG9 GLY A 1 UNP Q9YC86 EXPRESSION TAG SEQADV 7DG9 PRO A 2 UNP Q9YC86 EXPRESSION TAG SEQRES 1 A 93 GLY PRO MET ALA ASN SER SER VAL GLU LEU ARG VAL SER SEQRES 2 A 93 GLU ALA TYR PRO ARG ASP VAL GLY ARG LYS ILE VAL ARG SEQRES 3 A 93 ILE ASP ARG GLN THR ALA ALA ARG LEU GLY VAL GLU VAL SEQRES 4 A 93 GLY ASP PHE VAL LYS VAL SER LYS GLY ASP ARG SER VAL SEQRES 5 A 93 VAL ALA VAL VAL TRP PRO LEU ARG PRO ASP ASP GLU GLY SEQRES 6 A 93 ARG GLY ILE ILE ARG MET ASP GLY TYR LEU ARG ALA ALA SEQRES 7 A 93 LEU GLY VAL THR VAL GLY ASP THR VAL THR VAL GLU LYS SEQRES 8 A 93 ALA GLU HET ZN A 101 1 HET ZN A 102 1 HET ZN A 103 1 HET ZN A 104 1 HET ZN A 105 1 HETNAM ZN ZINC ION FORMUL 2 ZN 5(ZN 2+) FORMUL 7 HOH *138(H2 O) HELIX 1 AA1 TYR A 16 VAL A 20 5 5 HELIX 2 AA2 ASP A 28 GLY A 36 1 9 HELIX 3 AA3 ARG A 60 GLU A 64 5 5 HELIX 4 AA4 ASP A 72 GLY A 80 1 9 SHEET 1 AA1 7 SER A 7 SER A 13 0 SHEET 2 AA1 7 ILE A 68 ARG A 70 1 O ILE A 69 N SER A 13 SHEET 3 AA1 7 ILE A 24 ILE A 27 -1 N ARG A 26 O ARG A 70 SHEET 4 AA1 7 ARG A 50 PRO A 58 1 O TRP A 57 N VAL A 25 SHEET 5 AA1 7 PHE A 42 LYS A 47 -1 N VAL A 45 O VAL A 52 SHEET 6 AA1 7 THR A 86 LYS A 91 -1 O GLU A 90 N LYS A 44 SHEET 7 AA1 7 SER A 7 SER A 13 -1 N LEU A 10 O VAL A 87 LINK OE1 GLU A 9 ZN L ZN A 102 1555 1555 2.48 LINK OD1 ASP A 85 ZN L ZN A 104 1555 1555 2.22 LINK OD2 ASP A 85 ZN L ZN A 105 1555 1555 2.30 LINK OE2 GLU A 90 ZN L ZN A 101 1555 4556 2.02 LINK ZN L ZN A 101 O HOH A 229 1555 4456 2.30 LINK ZN L ZN A 101 O HOH A 233 1555 4456 2.25 LINK ZN L ZN A 103 O HOH A 243 1555 1565 2.25 LINK ZN L ZN A 103 O HOH A 316 1555 1555 2.36 LINK ZN L ZN A 103 O HOH A 330 1555 4566 2.41 LINK ZN L ZN A 104 O HOH A 235 1555 1555 2.22 LINK ZN L ZN A 104 O HOH A 296 1555 1555 2.03 LINK ZN L ZN A 104 O HOH A 299 1555 1545 2.28 LINK ZN L ZN A 104 O HOH A 310 1555 1555 2.16 LINK ZN L ZN A 105 O HOH A 335 1555 1545 2.66 CRYST1 26.040 31.066 94.156 90.00 90.00 90.00 P 21 21 21 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 0.038402 0.000000 0.000000 0.00000 SCALE2 0.000000 0.032190 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010621 0.00000