HEADER DNA BINDING PROTEIN 07-NOV-18 6N0S TITLE N-TERMINAL DOMAIN OF STAPHYLOTHERMUS MARINUS MCRB COMPND MOL_ID: 1; COMPND 2 MOLECULE: ATPASE ASSOCIATED WITH VARIOUS CELLULAR ACTIVITIES, AAA_5; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: N-TERMINAL DOMAIN (UNP RESIDUES 3-180); COMPND 5 SYNONYM: MCRB; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STAPHYLOTHERMUS MARINUS (STRAIN ATCC 43588 / SOURCE 3 DSM 3639 / JCM 9404 / F1); SOURCE 4 ORGANISM_TAXID: 399550; SOURCE 5 STRAIN: ATCC 43588 / DSM 3639 / JCM 9404 / F1; SOURCE 6 GENE: SMAR_0573; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS EVE DOMAIN, RESTRICTION ENDONUCLEASE, DNA BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR C.J.HOSFORD,Y.NIU,J.S.CHAPPIE REVDAT 3 25-NOV-20 6N0S 1 JRNL REVDAT 2 01-JAN-20 6N0S 1 REMARK REVDAT 1 13-NOV-19 6N0S 0 JRNL AUTH C.J.HOSFORD,M.C.ADAMS,Y.NIU,J.S.CHAPPIE JRNL TITL THE N-TERMINAL DOMAIN OF STAPHYLOTHERMUS MARINUS MCRB SHARES JRNL TITL 2 STRUCTURAL HOMOLOGY WITH PUA-LIKE RNA BINDING PROTEINS. JRNL REF J.STRUCT.BIOL. V. 211 07572 2020 JRNL REFN ESSN 1095-8657 JRNL PMID 32652237 JRNL DOI 10.1016/J.JSB.2020.107572 REMARK 2 REMARK 2 RESOLUTION. 1.92 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.92 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 55.26 REMARK 3 MIN(FOBS/SIGMA_FOBS) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 29031 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.196 REMARK 3 FREE R VALUE : 0.236 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL 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 0.0000 - 1.9200 0.00 0 0 0.0000 0.0000 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : NULL REMARK 3 SHRINKAGE RADIUS : NULL REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 6N0S COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 08-NOV-18. REMARK 100 THE DEPOSITION ID IS D_1000237967. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-AUG-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.3 - 7.7 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) : 0.9791 REMARK 200 MONOCHROMATOR : CRYO-COOLED DOUBLE CRYSTAL REMARK 200 SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 29031 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.920 REMARK 200 RESOLUTION RANGE LOW (A) : 55.260 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 42.20 REMARK 200 R MERGE (I) : 0.11100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 19.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.92 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.09 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 24.20 REMARK 200 R MERGE FOR SHELL (I) : 1.06800 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: SAD REMARK 200 SOFTWARE USED: SHELXCD REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.20 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.69 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M BIS-TRIS PROPANE, PH 7.5, 0.2 M REMARK 280 SODIUM SULFATE, 23% PEG3350, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 59.31650 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 31.20300 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 31.20300 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 88.97475 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 31.20300 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 31.20300 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 29.65825 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 31.20300 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 31.20300 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 88.97475 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 31.20300 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 31.20300 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 29.65825 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 59.31650 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 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 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 A 382 LIES ON A SPECIAL POSITION. 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 LYS A 88 O HOH A 301 1.96 REMARK 500 O ASN A 106 O HOH A 302 2.04 REMARK 500 O HOH A 368 O HOH A 390 2.14 REMARK 500 O SER A 66 O HOH A 303 2.17 REMARK 500 O HOH A 313 O HOH A 362 2.19 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 O3 SO4 A 202 O3 SO4 A 202 8665 1.97 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 PRO A 2 -160.12 -79.77 REMARK 500 MSE A 3 -50.95 -135.90 REMARK 500 ASN A 84 44.14 -144.85 REMARK 500 ARG A 125 71.40 45.47 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 SO4 A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 202 DBREF 6N0S A 4 181 UNP A3DM20 A3DM20_STAMF 3 180 SEQADV 6N0S GLY A 1 UNP A3DM20 EXPRESSION TAG SEQADV 6N0S PRO A 2 UNP A3DM20 EXPRESSION TAG SEQADV 6N0S MSE A 3 UNP A3DM20 EXPRESSION TAG SEQRES 1 A 181 GLY PRO MSE ASN LYS ILE LEU GLY PHE SER LYS TYR TRP SEQRES 2 A 181 VAL GLU ILE ASN ASN TRP ILE LEU PRO THR LEU ASP HIS SEQRES 3 A 181 ILE GLY LEU THR LEU TRP GLY MSE ILE LYS LYS HIS ALA SEQRES 4 A 181 SER GLU TYR ARG GLY ILE ARG TYR SER LEU GLU LYS PHE SEQRES 5 A 181 GLY GLU LEU LYS ILE ILE HIS TYR ILE GLY SER ARG ALA SEQRES 6 A 181 SER HIS ASP LEU GLY LYS THR PHE ILE GLY GLU SER VAL SEQRES 7 A 181 LEU SER LYS GLU ASN ASN LYS ILE VAL LYS GLU TYR SER SEQRES 8 A 181 TRP PRO GLU ILE LYS LYS VAL LEU ARG LYS ILE PHE LEU SEQRES 9 A 181 ASP ASN GLY ILE SER SER ASP THR ILE ASP GLN TYR PHE SEQRES 10 A 181 ILE ALA ILE ARG ARG ILE ILE ARG PRO SER ARG SER ASP SEQRES 11 A 181 ARG PHE PHE LEU PHE ARG LEU ALA GLU TYR ARG LYS TYR SEQRES 12 A 181 GLU ASN PRO VAL LYS TYR ASP GLN VAL ARG ASP ILE ILE SEQRES 13 A 181 SER HIS ILE THR TRP THR GLY ARG TYR LEU VAL PRO ILE SEQRES 14 A 181 ARG PRO GLU ASP TYR GLU ALA ILE HIS SER ARG GLY MODRES 6N0S MSE A 34 MET MODIFIED RESIDUE HET MSE A 3 8 HET MSE A 34 8 HET SO4 A 201 5 HET SO4 A 202 5 HETNAM MSE SELENOMETHIONINE HETNAM SO4 SULFATE ION FORMUL 1 MSE 2(C5 H11 N O2 SE) FORMUL 2 SO4 2(O4 S 2-) FORMUL 4 HOH *94(H2 O) HELIX 1 AA1 HIS A 38 GLY A 53 1 16 HELIX 2 AA2 SER A 63 SER A 66 5 4 HELIX 3 AA3 GLU A 82 LYS A 85 5 4 HELIX 4 AA4 SER A 91 ASN A 106 1 16 HELIX 5 AA5 SER A 109 ARG A 125 1 17 HELIX 6 AA6 ASP A 150 VAL A 152 5 3 HELIX 7 AA7 SER A 157 THR A 162 5 6 HELIX 8 AA8 ARG A 170 SER A 179 1 10 SHEET 1 AA1 5 ALA A 138 LYS A 148 0 SHEET 2 AA1 5 THR A 72 SER A 80 -1 N ILE A 74 O TYR A 143 SHEET 3 AA1 5 GLU A 54 ILE A 61 -1 N HIS A 59 O GLY A 75 SHEET 4 AA1 5 TYR A 12 ASN A 17 1 N GLU A 15 O TYR A 60 SHEET 5 AA1 5 LEU A 166 ILE A 169 -1 O VAL A 167 N VAL A 14 SHEET 1 AA2 3 THR A 30 MSE A 34 0 SHEET 2 AA2 3 PHE A 132 ARG A 136 -1 O PHE A 135 N LEU A 31 SHEET 3 AA2 3 GLU A 89 TYR A 90 -1 N TYR A 90 O PHE A 132 LINK C PRO A 2 N MSE A 3 1555 1555 1.32 LINK C MSE A 3 N ASN A 4 1555 1555 1.32 LINK C GLY A 33 N MSE A 34 1555 1555 1.32 LINK C MSE A 34 N ILE A 35 1555 1555 1.33 SITE 1 AC1 2 TRP A 32 TYR A 165 SITE 1 AC2 3 LYS A 5 SER A 40 ARG A 164 CRYST1 62.406 62.406 118.633 90.00 90.00 90.00 P 43 21 2 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 0.016024 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016024 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008429 0.00000