HEADER HYDROLASE 30-JUN-10 3NR1 TITLE A METAZOAN ORTHOLOG OF SPOT HYDROLYZES PPGPP AND PLAYS A ROLE IN TITLE 2 STARVATION RESPONSES COMPND MOL_ID: 1; COMPND 2 MOLECULE: HD DOMAIN-CONTAINING PROTEIN 3; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: METAZOAN SPOT HOMOLOG 1, MESH1; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: HDDC3; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET28(A) KEYWDS STRINGENT RESPONSE, PYROPHOSPHOHYDROLASE, HD (HISTIDINE AND ASPARTIC KEYWDS 2 ACID) FAMILY, PPGPP HYDROLASE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR D.W.SUN,H.Y.KIM,K.J.KIM,Y.H.JEON,J.CHUNG REVDAT 4 27-DEC-23 3NR1 1 REMARK LINK REVDAT 3 08-NOV-17 3NR1 1 REMARK REVDAT 2 09-OCT-13 3NR1 1 JRNL VERSN REVDAT 1 08-SEP-10 3NR1 0 JRNL AUTH D.W.SUN,G.LEE,J.H.LEE,H.Y.KIM,H.W.RHEE,S.Y.PARK,K.J.KIM, JRNL AUTH 2 Y.KIM,B.Y.KIM,J.I.HONG,C.PARK,H.E.CHOY,J.H.KIM,Y.H.JEON, JRNL AUTH 3 J.CHUNG JRNL TITL A METAZOAN ORTHOLOG OF SPOT HYDROLYZES PPGPP AND FUNCTIONS JRNL TITL 2 IN STARVATION RESPONSES JRNL REF NAT.STRUCT.MOL.BIOL. V. 17 1188 2010 JRNL REFN ISSN 1545-9993 JRNL PMID 20818390 JRNL DOI 10.1038/NSMB.1906 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 96.4 REMARK 3 NUMBER OF REFLECTIONS : 27178 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.203 REMARK 3 FREE R VALUE : 0.230 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 6.700 REMARK 3 FREE R VALUE TEST SET COUNT : 1890 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2850 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 2 REMARK 3 SOLVENT ATOMS : 220 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 24.39 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.17700 REMARK 3 B22 (A**2) : -0.36900 REMARK 3 B33 (A**2) : 0.19100 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 3.99700 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : NULL REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.225 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.838 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.296 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.499 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : 64.58 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : DNA-RNA_REP.PARAM REMARK 3 PARAMETER FILE 3 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 4 : ION.PARAM REMARK 3 PARAMETER FILE 5 : CARBOHYDRATE.PARAM REMARK 3 PARAMETER FILE 6 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : DNA-RNA.TOP REMARK 3 TOPOLOGY FILE 3 : WATER.TOP REMARK 3 TOPOLOGY FILE 4 : ION.TOP REMARK 3 TOPOLOGY FILE 5 : CARBOHYDRATE.TOP REMARK 3 TOPOLOGY FILE 6 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3NR1 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 22-JUL-10. REMARK 100 THE DEPOSITION ID IS D_1000060172. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-SEP-07; 06-MAR-08 REMARK 200 TEMPERATURE (KELVIN) : 293; NULL REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 2 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y; Y REMARK 200 RADIATION SOURCE : PAL/PLS; PAL/PLS REMARK 200 BEAMLINE : 4A; 6C1 REMARK 200 X-RAY GENERATOR MODEL : NULL; NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M; M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97953; 0.97955 REMARK 200 MONOCHROMATOR : NULL; NULL REMARK 200 OPTICS : NULL; NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD; CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210; ADSC QUANTUM REMARK 200 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO, HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK, HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 28330 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 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 (%) : 99.8 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : 0.07700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.97 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.5 REMARK 200 DATA REDUNDANCY IN SHELL : 3.50 REMARK 200 R MERGE FOR SHELL (I) : 0.35400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SAD; SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SOLVE 2.13, RESOLVE 2.13 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.86 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.23 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20-25% PEG 3350, 0.2M SODIUM CITRATE, REMARK 280 PH 7.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 296K 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 31.20000 REMARK 290 SMTRY3 2 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: 2440 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16660 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -13.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 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 MN A 199 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 35 NE2 REMARK 620 2 HIS A 61 NE2 89.3 REMARK 620 3 ASP A 62 OD2 103.1 72.1 REMARK 620 4 ASP A 122 OD1 79.9 98.4 169.8 REMARK 620 5 HOH A 304 O 112.2 157.5 95.6 92.1 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN B 199 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 35 NE2 REMARK 620 2 HIS B 61 NE2 87.4 REMARK 620 3 ASP B 62 OD2 101.0 68.5 REMARK 620 4 ASP B 122 OD1 82.0 100.1 167.9 REMARK 620 5 HOH B 275 O 102.8 165.9 99.7 91.0 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A 199 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN B 199 DBREF 3NR1 A 2 179 UNP Q8N4P3 HDDC3_HUMAN 2 179 DBREF 3NR1 B 2 179 UNP Q8N4P3 HDDC3_HUMAN 2 179 SEQRES 1 A 178 GLY SER GLU ALA ALA GLN LEU LEU GLU ALA ALA ASP PHE SEQRES 2 A 178 ALA ALA ARG LYS HIS ARG GLN GLN ARG ARG LYS ASP PRO SEQRES 3 A 178 GLU GLY THR PRO TYR ILE ASN HIS PRO ILE GLY VAL ALA SEQRES 4 A 178 ARG ILE LEU THR HIS GLU ALA GLY ILE THR ASP ILE VAL SEQRES 5 A 178 VAL LEU GLN ALA ALA LEU LEU HIS ASP THR VAL GLU ASP SEQRES 6 A 178 THR ASP THR THR LEU ASP GLU VAL GLU LEU HIS PHE GLY SEQRES 7 A 178 ALA GLN VAL ARG ARG LEU VAL GLU GLU VAL THR ASP ASP SEQRES 8 A 178 LYS THR LEU PRO LYS LEU GLU ARG LYS ARG LEU GLN VAL SEQRES 9 A 178 GLU GLN ALA PRO HIS SER SER PRO GLY ALA LYS LEU VAL SEQRES 10 A 178 LYS LEU ALA ASP LYS LEU TYR ASN LEU ARG ASP LEU ASN SEQRES 11 A 178 ARG CYS THR PRO GLU GLY TRP SER GLU HIS ARG VAL GLN SEQRES 12 A 178 GLU TYR PHE GLU TRP ALA ALA GLN VAL VAL LYS GLY LEU SEQRES 13 A 178 GLN GLY THR ASN ARG GLN LEU GLU GLU ALA LEU LYS HIS SEQRES 14 A 178 LEU PHE LYS GLN ARG GLY LEU THR ILE SEQRES 1 B 178 GLY SER GLU ALA ALA GLN LEU LEU GLU ALA ALA ASP PHE SEQRES 2 B 178 ALA ALA ARG LYS HIS ARG GLN GLN ARG ARG LYS ASP PRO SEQRES 3 B 178 GLU GLY THR PRO TYR ILE ASN HIS PRO ILE GLY VAL ALA SEQRES 4 B 178 ARG ILE LEU THR HIS GLU ALA GLY ILE THR ASP ILE VAL SEQRES 5 B 178 VAL LEU GLN ALA ALA LEU LEU HIS ASP THR VAL GLU ASP SEQRES 6 B 178 THR ASP THR THR LEU ASP GLU VAL GLU LEU HIS PHE GLY SEQRES 7 B 178 ALA GLN VAL ARG ARG LEU VAL GLU GLU VAL THR ASP ASP SEQRES 8 B 178 LYS THR LEU PRO LYS LEU GLU ARG LYS ARG LEU GLN VAL SEQRES 9 B 178 GLU GLN ALA PRO HIS SER SER PRO GLY ALA LYS LEU VAL SEQRES 10 B 178 LYS LEU ALA ASP LYS LEU TYR ASN LEU ARG ASP LEU ASN SEQRES 11 B 178 ARG CYS THR PRO GLU GLY TRP SER GLU HIS ARG VAL GLN SEQRES 12 B 178 GLU TYR PHE GLU TRP ALA ALA GLN VAL VAL LYS GLY LEU SEQRES 13 B 178 GLN GLY THR ASN ARG GLN LEU GLU GLU ALA LEU LYS HIS SEQRES 14 B 178 LEU PHE LYS GLN ARG GLY LEU THR ILE HET MN A 199 1 HET MN B 199 1 HETNAM MN MANGANESE (II) ION FORMUL 3 MN 2(MN 2+) FORMUL 5 HOH *220(H2 O) HELIX 1 1 SER A 3 HIS A 19 1 17 HELIX 2 2 ILE A 33 GLU A 46 1 14 HELIX 3 3 ASP A 51 HIS A 61 1 11 HELIX 4 4 ASP A 62 THR A 67 1 6 HELIX 5 5 THR A 70 VAL A 89 1 20 HELIX 6 6 PRO A 96 ALA A 108 1 13 HELIX 7 7 PRO A 109 SER A 111 5 3 HELIX 8 8 SER A 112 CYS A 133 1 22 HELIX 9 9 SER A 139 GLN A 158 1 20 HELIX 10 10 ASN A 161 GLN A 174 1 14 HELIX 11 11 SER B 3 HIS B 19 1 17 HELIX 12 12 ILE B 33 GLU B 46 1 14 HELIX 13 13 ASP B 51 HIS B 61 1 11 HELIX 14 14 ASP B 62 THR B 67 1 6 HELIX 15 15 THR B 70 VAL B 89 1 20 HELIX 16 16 PRO B 96 ALA B 108 1 13 HELIX 17 17 PRO B 109 SER B 111 5 3 HELIX 18 18 SER B 112 CYS B 133 1 22 HELIX 19 19 SER B 139 GLY B 156 1 18 HELIX 20 20 ASN B 161 ARG B 175 1 15 LINK NE2 HIS A 35 MN MN A 199 1555 1555 2.32 LINK NE2 HIS A 61 MN MN A 199 1555 1555 2.26 LINK OD2 ASP A 62 MN MN A 199 1555 1555 2.55 LINK OD1 ASP A 122 MN MN A 199 1555 1555 2.25 LINK MN MN A 199 O HOH A 304 1555 1555 2.31 LINK NE2 HIS B 35 MN MN B 199 1555 1555 2.35 LINK NE2 HIS B 61 MN MN B 199 1555 1555 2.28 LINK OD2 ASP B 62 MN MN B 199 1555 1555 2.56 LINK OD1 ASP B 122 MN MN B 199 1555 1555 2.22 LINK MN MN B 199 O HOH B 275 1555 1555 2.29 SITE 1 AC1 5 HIS A 35 HIS A 61 ASP A 62 ASP A 122 SITE 2 AC1 5 HOH A 304 SITE 1 AC2 5 HIS B 35 HIS B 61 ASP B 62 ASP B 122 SITE 2 AC2 5 HOH B 275 CRYST1 53.900 62.400 53.900 90.00 95.30 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 0.018553 0.000000 0.001721 0.00000 SCALE2 0.000000 0.016026 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018633 0.00000