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- PDB-3sc3: Crystal structure of a Putative DNA replication regulator Hda (Sa... -

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Basic information

Entry
Database: PDB / ID: 3sc3
TitleCrystal structure of a Putative DNA replication regulator Hda (Sama_1916) from SHEWANELLA AMAZONENSIS SB2B at 3.00 A resolution
ComponentsPutative DNA replication regulator Hda
KeywordsHYDROLASE REGULATOR / DNA BINDING PROTEIN / P-loop containing nucleoside triphosphate hydrolases / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY / HYDROLASE
Function / homology
Function and homology information


negative regulation of DNA-templated DNA replication initiation / DNA replication / nucleotide binding
Similarity search - Function
DnaA regulatory inactivator Hda / Chromosomal replication control, initiator DnaA-like / Chromosomal replication initiator protein DnaA / Bacterial dnaA protein / Helicase, Ruva Protein; domain 3 - #60 / Helicase, Ruva Protein; domain 3 / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / Orthogonal Bundle ...DnaA regulatory inactivator Hda / Chromosomal replication control, initiator DnaA-like / Chromosomal replication initiator protein DnaA / Bacterial dnaA protein / Helicase, Ruva Protein; domain 3 - #60 / Helicase, Ruva Protein; domain 3 / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Regulatory inactivation of DnaA Hda protein
Similarity search - Component
Biological speciesShewanella amazonensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.001 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a Putative DNA replication regulator Hda (Sama_1916) from SHEWANELLA AMAZONENSIS SB2B at 3.00 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJun 6, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 13, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_struct_assembly_auth_evidence / software
Revision 1.2Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.3Feb 1, 2023Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative DNA replication regulator Hda
B: Putative DNA replication regulator Hda
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,4987
Polymers51,0182
Non-polymers4805
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3310 Å2
ΔGint-96 kcal/mol
Surface area21000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)162.440, 162.440, 162.440
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number197
Space group name H-MI23
DetailsANALYTICAL SIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF A DIMER AS A SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION.

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Components

#1: Protein Putative DNA replication regulator Hda / Regulatory inactivation of DnaA Hda protein


Mass: 25509.047 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella amazonensis (bacteria) / Strain: SB2B / Gene: SAMA_14OCT04_CONTIG53_REVISED_GENE1514, Sama_1916 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: A1S6W5
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
Sequence detailsTHE CONSTRUCT (RESIDUES 18-241) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG ...THE CONSTRUCT (RESIDUES 18-241) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.5 Å3/Da / Density % sol: 64.86 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 1.26M (NH4)2SO4, 0.1M HEPES pH 7.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97799
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Nov 15, 2008
Details: Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (ho rizontal focusing)
RadiationMonochromator: single crystal Si(111) bent / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97799 Å / Relative weight: 1
ReflectionResolution: 3→46.881 Å / Num. obs: 14422 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 91.955 Å2 / Rmerge(I) obs: 0.143 / Net I/σ(I): 10.68
Reflection shell

Rmerge(I) obs: 0.014 / Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Mean I/σ(I) obsNum. measured obsNum. unique obs% possible all
3-3.171.616285217599.9
3.17-3.282.787451163100
3.28-3.413.691131211100
3.41-3.574.991401222100
3.57-3.767.593121239100
3.76-3.999.889671199100
3.99-4.2913.18984120099.9
4.29-4.7216.392191230100
4.72-5.3918.290771218100
5.39-6.7517.791911246100
6.7527.29314132499.4

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SHELXphasing
SHARPphasing
XSCALEDecember 6, 2007data scaling
PHENIX1.4refinement
XDSdata reduction
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 3.001→46.881 Å / Occupancy max: 1 / Occupancy min: 0.66 / SU ML: 1.17 / σ(F): 1.39 / Phase error: 27.67 / Stereochemistry target values: MLHL
Details: 1. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED ...Details: 1. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 2. SULFATE (SO4) MODELED ARE PRESENT IN CRYSTLLIZATION/CRYO CONDITION.
RfactorNum. reflection% reflection
Rfree0.2532 1449 10.06 %
Rwork0.2237 --
obs0.2267 14406 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 83.041 Å2 / ksol: 0.351 e/Å3
Displacement parametersBiso max: 199.91 Å2 / Biso mean: 121.4939 Å2 / Biso min: 86.54 Å2
Baniso -1Baniso -2Baniso -3
1--29.6512 Å2-0 Å2-0 Å2
2---29.6512 Å20 Å2
3----29.6512 Å2
Refinement stepCycle: LAST / Resolution: 3.001→46.881 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3310 0 25 0 3335
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023393
X-RAY DIFFRACTIONf_angle_d0.554591
X-RAY DIFFRACTIONf_chiral_restr0.035511
X-RAY DIFFRACTIONf_plane_restr0.002593
X-RAY DIFFRACTIONf_dihedral_angle_d14.6681255
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
3.001-3.10820.3841420.33112691411
3.1082-3.23250.35071410.322612901431
3.2325-3.37960.35321460.298612721418
3.3796-3.55760.33241440.283212811425
3.5576-3.78040.27391410.240312981439
3.7804-4.07190.29581440.225112911435
4.0719-4.48110.21411450.208412811426
4.4811-5.12830.23221480.184313061454
5.1283-6.4560.2161440.209613161460
6.456-38.29060.19431540.179913531507
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
1-0.1030.02960.0472-0.00950.08890.02331.51441.5546-1.2483-0.8519-0.0811.53610.1964-0.6946-0.00022.044-0.0410.52562.0654-0.47572.447340.369511.9674117.971
24.9755-2.445-0.7826.7755-0.67145.90250.1335-0.52950.45940.6432-0.044-0.0292-0.41270.045101.11180.0469-0.0921.2424-0.12981.235660.526410.6813116.9135
3-0.0270.09210.0773-0.1401-0.0090.0139-0.28570.0089-1.18750.27941.6830.69061.0831-2.524901.65330.1643-0.28282.33190.27331.720839.89133.2278120.2593
42.7534-1.991-0.7894.75060.91344.41680.3077-0.5373-0.50230.48790.0453-0.13120.24910.0864-01.47330.03520.12311.35810.22211.40123.45390.2123107.6912
50.12950.1149-0.06970.0079-0.07850.1402-0.1811-1.08690.445-0.1228-0.0698-2.0228-0.77760.2292-0.00011.71120.12550.01241.32710.01411.952534.342628.9727100.7788
64.2377-0.1442.76635.0511-0.60665.7466-0.0583-0.41850.48810.59080.12860.3744-0.4097-0.392601.14680.10630.07391.0291-0.01011.270818.105621.158597.1512
70.0487-0.10980.1071-0.0964-0.1666-0.05940.48611.1096-1.3206-1.307-0.4221-0.188-0.13960.885901.5727-0.0207-0.08091.38320.22861.9239.728124.741991.0132
82.6085-0.09521.33435.13310.17654.08710.24950.65020.3763-0.1276-0.16860.102-0.076-0.065-01.1462-0.01510.10091.31870.10141.235557.360712.873893.1299
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain A and resseq 30:35A30 - 35
2X-RAY DIFFRACTION2chain A and resseq 36:168A36 - 168
3X-RAY DIFFRACTION3chain A and resseq 169:175A169 - 175
4X-RAY DIFFRACTION4chain A and resseq 176:241A176 - 241
5X-RAY DIFFRACTION5chain B and resseq 31:38B31 - 38
6X-RAY DIFFRACTION6chain B and resseq 39:168B39 - 168
7X-RAY DIFFRACTION7chain B and resseq 169:175B169 - 175
8X-RAY DIFFRACTION8chain B and resseq 176:241B176 - 241

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