HEADER DNA BINDING PROTEIN 14-JAN-21 7DVN TITLE CRYSTAL STRUCTURE OF A MARR FAMILY PROTEIN IN COMPLEX WITH A LIPID- TITLE 2 LIKE EFFECTOR MOLECULE FROM THE PSYCHROPHILIC BACTERIUM TITLE 3 PAENISPOROSARCINA SP. TG-14 COMPND MOL_ID: 1; COMPND 2 MOLECULE: MARR FAMILY TRANSCRIPTIONAL REGULATOR; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: COMPLEX WITH PALMITIC ACID SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PAENISPOROSARCINA SP. TG-14; SOURCE 3 ORGANISM_TAXID: 1231057; SOURCE 4 GENE: E2636_00495; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS TRANSCRIPTION REGULATOR DNA-BINDING COMPLEX LIPID-LIKE EFFECTOR MARR KEYWDS 2 FAMILY, DNA BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR C.W.LEE,J.HWANG,H.DO,J.H.LEE REVDAT 2 29-MAY-24 7DVN 1 REMARK REVDAT 1 24-NOV-21 7DVN 0 JRNL AUTH J.HWANG,S.H.PARK,C.W.LEE,H.DO,S.C.SHIN,H.W.KIM,S.G.LEE, JRNL AUTH 2 H.H.PARK,S.KWON,J.H.LEE JRNL TITL CRYSTAL STRUCTURE OF A MARR FAMILY PROTEIN FROM THE JRNL TITL 2 PSYCHROPHILIC BACTERIUM PAENISPOROSARCINA SP. TG-14 IN JRNL TITL 3 COMPLEX WITH A LIPID-LIKE MOLECULE. JRNL REF IUCRJ V. 8 842 2021 JRNL REFN ESSN 2052-2525 JRNL PMID 34584745 JRNL DOI 10.1107/S2052252521005704 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 : CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.34 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.370 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 3 NUMBER OF REFLECTIONS : 26203 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.227 REMARK 3 R VALUE (WORKING SET) : 0.225 REMARK 3 FREE R VALUE : 0.255 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 1285 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 32.3400 - 3.3200 0.84 2547 140 0.2406 0.2727 REMARK 3 2 3.3200 - 2.6400 0.99 2847 131 0.2247 0.2251 REMARK 3 3 2.6400 - 2.3000 1.00 2847 143 0.2202 0.2606 REMARK 3 4 2.3000 - 2.0900 1.00 2792 162 0.2043 0.2500 REMARK 3 5 2.0900 - 1.9400 1.00 2804 142 0.2130 0.2605 REMARK 3 6 1.9400 - 1.8300 1.00 2785 140 0.2207 0.2484 REMARK 3 7 1.8300 - 1.7400 1.00 2784 146 0.2180 0.2494 REMARK 3 8 1.7400 - 1.6600 1.00 2762 148 0.2197 0.2558 REMARK 3 9 1.6600 - 1.6000 1.00 2750 133 0.2321 0.2694 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) : 0.166 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.122 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 23.63 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 28.78 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 : 0.017 1127 REMARK 3 ANGLE : 1.871 1504 REMARK 3 CHIRALITY : 0.106 180 REMARK 3 PLANARITY : 0.014 182 REMARK 3 DIHEDRAL : 24.852 450 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 7DVN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 18-JAN-21. REMARK 100 THE DEPOSITION ID IS D_1300020268. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-NOV-18 REMARK 200 TEMPERATURE (KELVIN) : 95 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PAL/PLS REMARK 200 BEAMLINE : 5C (4A) REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9794 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER2 X 9M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 26268 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 (%) : 98.0 REMARK 200 DATA REDUNDANCY : 26.40 REMARK 200 R MERGE (I) : 0.07400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 82.4000 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) : 1.63 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.42200 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 (%): 57.02 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.86 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.6M AMMONIUM CITRATE TRIBASIC, PH REMARK 280 7.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 296K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 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+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 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 45.15500 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 32.76200 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 32.76200 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 22.57750 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 32.76200 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 32.76200 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 67.73250 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 32.76200 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 32.76200 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 22.57750 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 32.76200 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 32.76200 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 67.73250 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 45.15500 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: 8710 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13270 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -50.0 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 350 BIOMT1 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 -45.15500 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 393 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 441 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 GLY A 50 REMARK 465 GLU A 51 REMARK 465 PRO A 85 REMARK 465 SER A 86 REMARK 465 GLY A 87 REMARK 465 ASP A 88 REMARK 465 LYS A 89 REMARK 465 ARG A 90 REMARK 465 GLU A 91 REMARK 465 LYS A 92 REMARK 465 GLY A 146 REMARK 465 VAL A 147 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 LYS A 48 -84.94 -81.87 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 PLM A 201 DBREF 7DVN A 1 147 PDB 7DVN 7DVN 1 147 SEQRES 1 A 147 MET ASP LYS ARG ILE GLN GLU ALA VAL SER LEU PHE GLU SEQRES 2 A 147 GLU VAL LEU ILE TYR GLY THR GLU ARG VAL ILE ARG SER SEQRES 3 A 147 VAL ASP ASP PRO LEU TRP ARG GLU TYR SER PRO GLU GLN SEQRES 4 A 147 MET GLN VAL LEU LYS LEU ILE TYR LYS GLU GLY GLU ILE SEQRES 5 A 147 THR SER GLY ARG LEU ALA ILE LEU GLN GLY VAL HIS LYS SEQRES 6 A 147 SER ALA ILE SER ASN ARG LEU LYS LYS LEU ILE GLU LYS SEQRES 7 A 147 GLU VAL ILE SER ILE LYS PRO SER GLY ASP LYS ARG GLU SEQRES 8 A 147 LYS ILE LEU VAL LEU THR ALA LEU GLY GLU THR VAL ILE SEQRES 9 A 147 LYS GLN SER ASP ALA VAL LEU HIS GLU TYR ILE GLY LYS SEQRES 10 A 147 LEU MET THR ASN LYS VAL ASP ASP GLN GLU ILE GLU GLN SEQRES 11 A 147 PHE LEU VAL THR PHE ARG LYS LEU LYS GLU ILE LEU LYS SEQRES 12 A 147 MET ASN GLY VAL HET PLM A 201 18 HETNAM PLM PALMITIC ACID FORMUL 2 PLM C16 H32 O2 FORMUL 3 HOH *143(H2 O) HELIX 1 AA1 ASP A 2 VAL A 27 1 26 HELIX 2 AA2 PRO A 30 TYR A 35 1 6 HELIX 3 AA3 SER A 36 LYS A 48 1 13 HELIX 4 AA4 THR A 53 GLY A 62 1 10 HELIX 5 AA5 HIS A 64 LYS A 78 1 15 HELIX 6 AA6 THR A 97 THR A 120 1 24 HELIX 7 AA7 ASP A 124 LYS A 143 1 20 SHEET 1 AA1 2 ILE A 81 SER A 82 0 SHEET 2 AA1 2 VAL A 95 LEU A 96 -1 O VAL A 95 N SER A 82 SITE 1 AC1 1 GLU A 13 CRYST1 65.524 65.524 90.310 90.00 90.00 90.00 P 41 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 0.015262 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015262 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011073 0.00000