HEADER CHAPERONE 20-JAN-21 7DXY TITLE CRYSTAL STRUCTURE OF THE CHEMICALLY SYNTHESIZED MK2H_DELTAMILPS TITLE 2 PEPTIDE HOMODIMER COMPND MOL_ID: 1; COMPND 2 MOLECULE: MK2H_DELTAMILPS; COMPND 3 CHAIN: B, A; 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; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS DOUBLE PSI BETA BARREL, CHAPERONE EXPDTA X-RAY DIFFRACTION AUTHOR S.YAGI,S.TAGAMI REVDAT 3 29-NOV-23 7DXY 1 JRNL REVDAT 2 17-NOV-21 7DXY 1 JRNL REVDAT 1 29-SEP-21 7DXY 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 ISSN 2692-8205 REMARK 1 DOI 10.1101/2021.02.22.432383 REMARK 2 REMARK 2 RESOLUTION. 1.40 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) : 1.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.26 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.470 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 15896 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.213 REMARK 3 R VALUE (WORKING SET) : 0.211 REMARK 3 FREE R VALUE : 0.230 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.020 REMARK 3 FREE R VALUE TEST SET COUNT : 1592 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 24.2630 - 3.1116 0.95 1356 152 0.1908 0.2227 REMARK 3 2 3.1116 - 2.4705 1.00 1336 150 0.2110 0.2137 REMARK 3 3 2.4705 - 2.1585 0.99 1311 145 0.1961 0.2465 REMARK 3 4 2.1585 - 1.9612 1.00 1322 147 0.1976 0.1884 REMARK 3 5 1.9612 - 1.8207 0.99 1284 142 0.2300 0.2217 REMARK 3 6 1.8207 - 1.7134 0.99 1285 144 0.2355 0.2363 REMARK 3 7 1.7134 - 1.6276 0.99 1291 144 0.2542 0.2987 REMARK 3 8 1.6276 - 1.5568 1.00 1292 142 0.2559 0.2440 REMARK 3 9 1.5568 - 1.4968 1.00 1288 143 0.2763 0.2821 REMARK 3 10 1.4968 - 1.4452 1.00 1286 144 0.2961 0.2958 REMARK 3 11 1.4452 - 1.4000 1.00 1253 139 0.3257 0.3184 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) : 0.130 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 29.150 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 31.18 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 7DXY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 21-JAN-21. REMARK 100 THE DEPOSITION ID IS D_1300020276. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-SEP-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 : SLS REMARK 200 BEAMLINE : X06SA 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 : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17566 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.350 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 (%) : 99.2 REMARK 200 DATA REDUNDANCY : 6.260 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 18.8500 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.35 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.44 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: 7DXX REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.03 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.02 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 400MM SODIUM PHOSPHATE REMARK 280 MONOBASIC/1600MM POTTASIUM PHOSPHATE DIBASIC, 100 MM IMIDAZOLE_ REMARK 280 HCL, PH 8.0, 200 MM NACL, 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 15.33000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 32.14150 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 19.84400 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 32.14150 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 15.33000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 19.84400 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4350 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 4720 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -17.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, 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 LYS B 4 REMARK 465 LYS A 4 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 B 114 O HOH B 147 1.76 REMARK 500 NZ LYS A 45 O HOH A 101 1.78 REMARK 500 O HOH A 137 O HOH A 138 1.95 REMARK 500 O HOH A 108 O HOH A 145 1.98 REMARK 500 N LYS A 5 O HOH A 102 2.04 REMARK 500 O HOH B 120 O HOH B 135 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 B 141 O HOH A 139 3645 2.18 REMARK 500 REMARK 500 REMARK: NULL DBREF 7DXY B 4 46 PDB 7DXY 7DXY 4 46 DBREF 7DXY A 4 46 PDB 7DXY 7DXY 4 46 SEQRES 1 B 43 LYS LYS VAL VAL ALA ARG VAL ALA GLU ALA TYR ALA GLU SEQRES 2 B 43 ASP VAL GLY LYS ARG VAL VAL ARG VAL ASP LYS TYR GLU SEQRES 3 B 43 ARG ALA LYS VAL GLY VAL LYS VAL GLY ASP TYR VAL GLU SEQRES 4 B 43 VAL LYS LYS VAL SEQRES 1 A 43 LYS LYS VAL VAL ALA ARG VAL ALA GLU ALA TYR ALA GLU SEQRES 2 A 43 ASP VAL GLY LYS ARG VAL VAL ARG VAL ASP LYS TYR GLU SEQRES 3 A 43 ARG ALA LYS VAL GLY VAL LYS VAL GLY ASP TYR VAL GLU SEQRES 4 A 43 VAL LYS LYS VAL FORMUL 3 HOH *96(H2 O) HELIX 1 AA1 TYR B 14 VAL B 18 5 5 HELIX 2 AA2 ASP B 26 GLY B 34 1 9 HELIX 3 AA3 TYR A 14 VAL A 18 5 5 HELIX 4 AA4 ASP A 26 GLY A 34 1 9 SHEET 1 AA1 7 VAL B 6 GLU B 12 0 SHEET 2 AA1 7 VAL A 22 VAL A 25 1 O VAL A 23 N ARG B 9 SHEET 3 AA1 7 VAL B 22 VAL B 25 -1 N ARG B 24 O ARG A 24 SHEET 4 AA1 7 VAL A 6 GLU A 12 1 O ARG A 9 N VAL B 23 SHEET 5 AA1 7 TYR B 40 LYS B 45 -1 N VAL B 43 O VAL A 6 SHEET 6 AA1 7 TYR A 40 LYS A 45 -1 O GLU A 42 N LYS B 44 SHEET 7 AA1 7 VAL B 6 GLU B 12 -1 N VAL B 6 O VAL A 43 CRYST1 30.660 39.688 64.283 90.00 90.00 90.00 P 21 21 21 8 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 0.032616 0.000000 0.000000 0.00000 SCALE2 0.000000 0.025197 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015556 0.00000