HEADER CHAPERONE 18-NOV-20 7DI1 TITLE CRYSTAL STRUCTURE OF THE RATIONALLY DESIGNED MKDPBB_SYM_86 PROTEIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: MKDPBB_SYM_86 PROTEIN; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 3 ORGANISM_TAXID: 32630; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS DOUBLE PSI BETA BARREL, CHAPERONE EXPDTA X-RAY DIFFRACTION AUTHOR S.YAGI,S.TAGAMI REVDAT 3 29-NOV-23 7DI1 1 REMARK REVDAT 2 17-NOV-21 7DI1 1 JRNL REVDAT 1 29-SEP-21 7DI1 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 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.11.1_2575 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) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.46 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 83.1 REMARK 3 NUMBER OF REFLECTIONS : 8352 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.211 REMARK 3 R VALUE (WORKING SET) : 0.205 REMARK 3 FREE R VALUE : 0.264 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.010 REMARK 3 FREE R VALUE TEST SET COUNT : 836 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 30.4550 - 3.8091 0.94 1424 165 0.1742 0.2188 REMARK 3 2 3.8091 - 3.0242 0.84 1261 144 0.1980 0.2716 REMARK 3 3 3.0242 - 2.6422 0.97 1205 130 0.2281 0.3028 REMARK 3 4 2.6422 - 2.4007 0.95 1393 142 0.2312 0.2914 REMARK 3 5 2.4007 - 2.2287 0.93 972 114 0.2254 0.2956 REMARK 3 6 2.2287 - 2.0973 0.92 1261 141 0.2625 0.3087 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) : 0.280 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 28.430 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.69 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 : 0.008 1456 REMARK 3 ANGLE : 1.078 1952 REMARK 3 CHIRALITY : 0.066 216 REMARK 3 PLANARITY : 0.005 244 REMARK 3 DIHEDRAL : 21.341 588 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 7DI1 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 23-NOV-20. REMARK 100 THE DEPOSITION ID IS D_1300019427. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-NOV-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 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 : 8524 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.097 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 (%) : 84.8 REMARK 200 DATA REDUNDANCY : 7.670 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.22 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: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 7DG7 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.97 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.16 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100MM HEPES PH 7.0, 15% PEG 20000, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K 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 42.65100 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 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 APPLY THE FOLLOWING TO CHAINS: B 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 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 GLY A 3 O HOH A 201 1.82 REMARK 500 NZ LYS A 7 O HOH A 202 1.84 REMARK 500 SD MET A 25 O HOH A 249 1.85 REMARK 500 O HOH A 250 O HOH A 251 1.94 REMARK 500 OE2 GLU B 16 O HOH B 201 1.95 REMARK 500 O HOH A 213 O HOH A 250 2.01 REMARK 500 O HOH A 244 O HOH B 221 2.02 REMARK 500 O MET B 1 O HOH B 202 2.06 REMARK 500 OE2 GLU A 16 O HOH A 203 2.08 REMARK 500 NE ARG A 52 O HOH A 204 2.14 REMARK 500 O HOH A 213 O HOH A 251 2.19 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 VAL A 46 -59.18 48.18 REMARK 500 VAL B 46 -63.37 66.48 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EPE A 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EPE B 101 DBREF 7DI1 A -1 90 PDB 7DI1 7DI1 -1 90 DBREF 7DI1 B -1 90 PDB 7DI1 7DI1 -1 90 SEQRES 1 A 92 GLY PRO MET PRO GLY LEU SER VAL LYS LEU ARG VAL ALA SEQRES 2 A 92 GLU ALA TYR PRO GLU ASP VAL GLY LYS ARG ILE VAL ARG SEQRES 3 A 92 MET ASP LYS ALA SER ARG ALA LYS LEU GLY VAL SER VAL SEQRES 4 A 92 GLY ASP TYR VAL GLU VAL LYS LYS VAL LYS SER VAL VAL SEQRES 5 A 92 ALA ARG VAL ALA GLU ALA TYR PRO GLU ASP VAL GLY LYS SEQRES 6 A 92 GLY ILE VAL ARG MET ASP LYS TYR GLU ARG ALA LYS LEU SEQRES 7 A 92 GLY VAL SER VAL GLY ASP TYR VAL GLU VAL LYS LYS VAL SEQRES 8 A 92 GLU SEQRES 1 B 92 GLY PRO MET PRO GLY LEU SER VAL LYS LEU ARG VAL ALA SEQRES 2 B 92 GLU ALA TYR PRO GLU ASP VAL GLY LYS ARG ILE VAL ARG SEQRES 3 B 92 MET ASP LYS ALA SER ARG ALA LYS LEU GLY VAL SER VAL SEQRES 4 B 92 GLY ASP TYR VAL GLU VAL LYS LYS VAL LYS SER VAL VAL SEQRES 5 B 92 ALA ARG VAL ALA GLU ALA TYR PRO GLU ASP VAL GLY LYS SEQRES 6 B 92 GLY ILE VAL ARG MET ASP LYS TYR GLU ARG ALA LYS LEU SEQRES 7 B 92 GLY VAL SER VAL GLY ASP TYR VAL GLU VAL LYS LYS VAL SEQRES 8 B 92 GLU HET EPE A 101 15 HET EPE B 101 15 HETNAM EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID HETSYN EPE HEPES FORMUL 3 EPE 2(C8 H18 N2 O4 S) FORMUL 5 HOH *93(H2 O) HELIX 1 AA1 TYR A 14 VAL A 18 5 5 HELIX 2 AA2 ASP A 26 LEU A 33 1 8 HELIX 3 AA3 TYR A 57 VAL A 61 5 5 HELIX 4 AA4 ASP A 69 GLY A 77 1 9 HELIX 5 AA5 TYR B 14 VAL B 18 5 5 HELIX 6 AA6 ASP B 26 GLY B 34 1 9 HELIX 7 AA7 TYR B 57 VAL B 61 5 5 HELIX 8 AA8 ASP B 69 GLY B 77 1 9 SHEET 1 AA1 7 VAL A 6 ALA A 11 0 SHEET 2 AA1 7 ILE A 65 ARG A 67 1 O VAL A 66 N ALA A 11 SHEET 3 AA1 7 ILE A 22 MET A 25 -1 N ARG A 24 O ARG A 67 SHEET 4 AA1 7 SER A 48 GLU A 55 1 O ALA A 54 N VAL A 23 SHEET 5 AA1 7 TYR A 40 LYS A 44 -1 N VAL A 43 O VAL A 49 SHEET 6 AA1 7 TYR A 83 LYS A 88 -1 O LYS A 87 N GLU A 42 SHEET 7 AA1 7 VAL A 6 ALA A 11 -1 N VAL A 6 O VAL A 86 SHEET 1 AA2 7 VAL B 6 ALA B 11 0 SHEET 2 AA2 7 ILE B 65 ARG B 67 1 O VAL B 66 N ARG B 9 SHEET 3 AA2 7 ILE B 22 MET B 25 -1 N ARG B 24 O ARG B 67 SHEET 4 AA2 7 SER B 48 GLU B 55 1 O ALA B 54 N VAL B 23 SHEET 5 AA2 7 TYR B 40 LYS B 44 -1 N VAL B 43 O VAL B 49 SHEET 6 AA2 7 TYR B 83 LYS B 88 -1 O LYS B 87 N GLU B 42 SHEET 7 AA2 7 VAL B 6 ALA B 11 -1 N LEU B 8 O VAL B 84 SITE 1 AC1 6 ALA A 13 VAL A 18 ASP A 69 LYS A 70 SITE 2 AC1 6 ARG A 73 HOH A 209 SITE 1 AC2 8 GLU B 12 ALA B 13 VAL B 18 MET B 68 SITE 2 AC2 8 ASP B 69 LYS B 70 ARG B 73 HOH B 237 CRYST1 31.238 85.302 32.604 90.00 90.00 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 0.032012 0.000000 0.000001 0.00000 SCALE2 0.000000 0.011723 0.000000 0.00000 SCALE3 0.000000 0.000000 0.030671 0.00000