HEADER TRANSFERASE 12-MAR-21 7ECD TITLE CRYSTAL STRUCTURE OF TAM41 FROM FIRMICUTES BACTERIUM, COMPLEX WITH TITLE 2 CTP-MG COMPND MOL_ID: 1; COMPND 2 MOLECULE: PHOSPHATIDATE CYTIDYLYLTRANSFERASE; COMPND 3 CHAIN: A; COMPND 4 EC: 2.7.7.41; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: FIRMICUTES BACTERIUM CAG:884; SOURCE 3 ORGANISM_TAXID: 1262990; SOURCE 4 GENE: BN804_00706; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_VARIANT: C41 KEYWDS CDP-DAG SYNTHASE, PHOSPHATIDIC ACID, CYTIDINE-DIPHOSPHATE KEYWDS 2 DIACYLGLYCEROL, MITOCHONDRIAL MATRIX, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR K.KIMURA,F.KAWAI,H.KUBOTA-KAWAI,Y.WATANABE,Y.TAMURA REVDAT 2 13-APR-22 7ECD 1 JRNL REVDAT 1 19-JAN-22 7ECD 0 JRNL AUTH K.KIMURA,F.KAWAI,H.KUBOTA-KAWAI,Y.WATANABE,K.TOMII,R.KOJIMA, JRNL AUTH 2 K.HIRATA,Y.YAMAMORI,T.ENDO,Y.TAMURA JRNL TITL CRYSTAL STRUCTURE OF TAM41 CYTIDINE DIPHOSPHATE JRNL TITL 2 DIACYLGLYCEROL SYNTHASE FROM A FIRMICUTES BACTERIUM. JRNL REF J.BIOCHEM. V. 171 429 2022 JRNL REFN ISSN 0021-924X JRNL PMID 34964897 JRNL DOI 10.1093/JB/MVAB154 REMARK 2 REMARK 2 RESOLUTION. 2.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.17_3644: ???) 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) : 2.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.12 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 18728 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.203 REMARK 3 R VALUE (WORKING SET) : 0.201 REMARK 3 FREE R VALUE : 0.238 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.830 REMARK 3 FREE R VALUE TEST SET COUNT : 904 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 43.1200 - 4.7200 1.00 3020 151 0.1744 0.1888 REMARK 3 2 4.7200 - 3.7500 1.00 2983 143 0.1758 0.2264 REMARK 3 3 3.7500 - 3.2700 1.00 2948 176 0.2169 0.2681 REMARK 3 4 3.2700 - 2.9700 1.00 2987 133 0.2525 0.3115 REMARK 3 5 2.9700 - 2.7600 1.00 2924 157 0.2785 0.2775 REMARK 3 6 2.7600 - 2.6000 0.99 2962 144 0.3516 0.4184 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) : 0.450 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 28.250 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 : 0.008 2334 REMARK 3 ANGLE : 1.065 3141 REMARK 3 CHIRALITY : 0.055 327 REMARK 3 PLANARITY : 0.005 400 REMARK 3 DIHEDRAL : 22.469 311 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 7ECD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 23-MAR-21. REMARK 100 THE DEPOSITION ID IS D_1300021033. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-NOV-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 : BL32XU REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.92 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 9M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 36822 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.600 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 (%) : 99.7 REMARK 200 DATA REDUNDANCY : 13.50 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 23.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.76 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: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 74.49 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.82 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M HEPES PH 7.0, 13-15% (W/V) PEG REMARK 280 6000, 10% (V/V) GLYCEROL, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 41 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 3555 -Y,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X,Z+3/4 REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X,-Y,Z REMARK 290 7555 -Y+1/2,X,Z+3/4 REMARK 290 8555 Y,-X+1/2,Z+1/4 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 52.07950 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 52.07950 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 56.97950 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 52.07950 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 28.48975 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 52.07950 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 85.46925 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 52.07950 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 52.07950 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 56.97950 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 7 0.000000 -1.000000 0.000000 52.07950 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 85.46925 REMARK 290 SMTRY1 8 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 52.07950 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 28.48975 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: 820 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13390 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -13.0 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 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 SER A 33 153.47 -44.99 REMARK 500 LYS A 34 23.01 80.08 REMARK 500 LYS A 36 76.09 39.99 REMARK 500 ASP A 236 71.32 -151.21 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 MG A 302 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 40 OD1 REMARK 620 2 ASP A 40 OD2 53.9 REMARK 620 3 CTP A 301 O1A 112.0 102.8 REMARK 620 4 CTP A 301 O1B 86.5 138.2 78.1 REMARK 620 5 CTP A 301 O1G 152.8 152.5 75.1 68.9 REMARK 620 N 1 2 3 4 DBREF 7ECD A 1 265 UNP R5MX27 R5MX27_9FIRM 1 265 SEQADV 7ECD MET A -6 UNP R5MX27 INITIATING METHIONINE SEQADV 7ECD HIS A -5 UNP R5MX27 EXPRESSION TAG SEQADV 7ECD HIS A -4 UNP R5MX27 EXPRESSION TAG SEQADV 7ECD HIS A -3 UNP R5MX27 EXPRESSION TAG SEQADV 7ECD HIS A -2 UNP R5MX27 EXPRESSION TAG SEQADV 7ECD HIS A -1 UNP R5MX27 EXPRESSION TAG SEQADV 7ECD HIS A 0 UNP R5MX27 EXPRESSION TAG SEQRES 1 A 272 MET HIS HIS HIS HIS HIS HIS MET LYS ASP PHE ILE LYS SEQRES 2 A 272 GLU PHE LEU ASN GLU ARG PRO GLU VAL VAL ALA ALA PHE SEQRES 3 A 272 GLY TYR GLY SER GLY VAL PHE LYS GLN LEU GLY TYR ASP SEQRES 4 A 272 SER LYS GLU LYS PRO GLN ILE ASP LEU ILE LEU ILE VAL SEQRES 5 A 272 ASN ASP MET LYS LEU TRP HIS LYS GLU ASN ILE LYS LYS SEQRES 6 A 272 ASN PRO LYS ASP TYR SER PHE ILE GLY ARG ASN PHE PHE SEQRES 7 A 272 LEU ASN SER SER ILE ASP GLU ILE LYS GLY ILE THR GLY SEQRES 8 A 272 ILE THR TYR GLN SER ASN ILE GLU TYR LYS GLY HIS LEU SEQRES 9 A 272 PHE LYS TYR GLY ILE ILE GLU TYR GLY ASP PHE VAL ARG SEQRES 10 A 272 HIS MET GLN THR TRP ASP SER PHE TYR VAL PRO GLY ARG SEQRES 11 A 272 PHE GLN LYS PRO ILE LEU THR ILE LYS SER ASN ASN PHE SEQRES 12 A 272 ILE ASP GLU LEU ILE LEU GLN ASN ARG ARG ASN ALA CYS SEQRES 13 A 272 LYS VAL GLY LEU LEU CYS LEU ASN ASN LYS ASP LEU LYS SEQRES 14 A 272 ASP LEU TYR LEU THR ILE CYS ASN LEU SER TYR SER GLY SEQRES 15 A 272 ASP THR ARG MET LYS VAL ALA GLU ASN PRO LYS LYS VAL SEQRES 16 A 272 GLU ASN ILE VAL GLY ALA SER TYR ASP LYS PHE ASN GLU SEQRES 17 A 272 MET TYR ASN PHE ASN ASP LEU TYR GLN LYS ASN GLY GLU SEQRES 18 A 272 ARG ILE GLU TYR GLU ILE ASP ILE ASP GLU LEU PRO SER SEQRES 19 A 272 SER LEU GLU LYS TYR ILE LYS ASP ASP LYS THR LYS GLU SEQRES 20 A 272 LYS VAL MET GLU TYR LEU SER ASP LEU ASN ARG LYS GLU SEQRES 21 A 272 SER SER LEU GLN THR MET LYS GLY ILE LYS THR ASN HET CTP A 301 29 HET MG A 302 1 HET BR A 303 1 HET BR A 304 1 HETNAM CTP CYTIDINE-5'-TRIPHOSPHATE HETNAM MG MAGNESIUM ION HETNAM BR BROMIDE ION FORMUL 2 CTP C9 H16 N3 O14 P3 FORMUL 3 MG MG 2+ FORMUL 4 BR 2(BR 1-) FORMUL 6 HOH *2(H2 O) HELIX 1 AA1 HIS A -4 GLU A 11 1 16 HELIX 2 AA2 ASP A 47 ASN A 59 1 13 HELIX 3 AA3 PRO A 60 TYR A 63 5 4 HELIX 4 AA4 SER A 64 SER A 74 1 11 HELIX 5 AA5 SER A 75 GLY A 81 1 7 HELIX 6 AA6 TYR A 105 TRP A 115 1 11 HELIX 7 AA7 PHE A 118 PHE A 124 1 7 HELIX 8 AA8 ASN A 134 LEU A 156 1 23 HELIX 9 AA9 ASP A 160 LEU A 171 1 12 HELIX 10 AB1 ALA A 182 SER A 195 1 14 HELIX 11 AB2 SER A 195 TYR A 203 1 9 HELIX 12 AB3 PRO A 226 ILE A 233 1 8 HELIX 13 AB4 THR A 238 LYS A 263 1 26 SHEET 1 AA1 5 ILE A 85 TYR A 93 0 SHEET 2 AA1 5 HIS A 96 GLU A 104 -1 O PHE A 98 N ILE A 91 SHEET 3 AA1 5 ILE A 39 VAL A 45 1 N LEU A 43 O GLY A 101 SHEET 4 AA1 5 ALA A 17 TYR A 21 -1 N TYR A 21 O ASP A 40 SHEET 5 AA1 5 LEU A 129 LYS A 132 -1 O LEU A 129 N GLY A 20 SHEET 1 AA2 2 TYR A 209 ASN A 212 0 SHEET 2 AA2 2 ARG A 215 TYR A 218 -1 O GLU A 217 N GLN A 210 LINK OD1 ASP A 40 MG MG A 302 1555 1555 2.13 LINK OD2 ASP A 40 MG MG A 302 1555 1555 2.58 LINK O1A CTP A 301 MG MG A 302 1555 1555 1.93 LINK O1B CTP A 301 MG MG A 302 1555 1555 2.35 LINK O1G CTP A 301 MG MG A 302 1555 1555 2.24 CRYST1 104.159 104.159 113.959 90.00 90.00 90.00 I 41 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 0.009601 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009601 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008775 0.00000