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- PDB-5he9: Bacterial initiation protein in complex with Phage inhibitor protein -

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Basic information

Entry
Database: PDB / ID: 5he9
TitleBacterial initiation protein in complex with Phage inhibitor protein
Components
  • Helicase loader
  • Phage inhibitor protein
KeywordsPROTEIN BINDING / inhibitor protein complex
Function / homology
Function and homology information


DNA replication / nucleotide binding / metal ion binding
Similarity search - Function
Primosomal DnaI, N-terminal / Primosomal protein DnaI N-terminus / Chromosomal replication initiator protein DnaA / Bacterial DnaA ATPAse domain / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / BERYLLIUM TRIFLUORIDE ION / : / Primosomal protein DnaI / 77ORF104 / DnaI
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
Staphylococcus aureus subsp. aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsHood, I.V. / Berger, J.M.
CitationJournal: To Be Published
Title: Structure of inhibited replicative helicase loader from Staphylococcus aureus at 1.9 Angstrom resolution
Authors: Hood, I.V. / Berger, J.M.
History
DepositionJan 5, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 8, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_oper_list / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Helicase loader
E: Phage inhibitor protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,0115
Polymers26,4942
Non-polymers5183
Water3,639202
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3310 Å2
ΔGint-30 kcal/mol
Surface area11420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.173, 73.173, 189.727
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

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Protein , 2 types, 2 molecules AE

#1: Protein Helicase loader / Primosomal protein DnaI


Mass: 19888.043 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: dnaI / Production host: Escherichia coli (E. coli) / References: UniProt: W8TSU2, UniProt: Q2FXP5*PLUS
#2: Protein Phage inhibitor protein


Mass: 6605.570 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus (bacteria)
Gene: OO23_07105 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0J7LG86, UniProt: Q6R837*PLUS

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Non-polymers , 4 types, 205 molecules

#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Chemical ChemComp-BEF / BERYLLIUM TRIFLUORIDE ION


Mass: 66.007 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: BeF3
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 202 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.85 Å3/Da / Density % sol: 56.85 %
Crystal growTemperature: 294.15 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 50 mM Tris-HCl 8.5, 20 mM MgCl2, 20% ethanol / PH range: 8.5

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 26, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.9→48.13 Å / % possible obs: 99.9 % / Redundancy: 13.2 % / Net I/σ(I): 3.4

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.9→44.764 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.11 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.2177 2274 5.09 %Random selection
Rwork0.1823 ---
obs0.1841 44704 99.79 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→44.764 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1791 0 32 202 2025
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0121863
X-RAY DIFFRACTIONf_angle_d1.3352515
X-RAY DIFFRACTIONf_dihedral_angle_d14.485700
X-RAY DIFFRACTIONf_chiral_restr0.054278
X-RAY DIFFRACTIONf_plane_restr0.006318
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Highest resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.9-1.94130.44141760.3967251697
1.9413-1.98651462681100
1.9865-2.03620.25981480.2522657100
2.0362-2.09120.26311150.2332677100
2.0912-2.15281322692100
2.1528-2.22220.2641520.2062628100
2.2222-2.30170.28051390.24592656100
2.3017-2.39380.23571090.19062695100
2.3938-2.50270.20861490.17622629100
2.5027-2.63470.19071710.18172632100
2.6347-2.79970.21521380.17822677100
2.7997-3.01590.24171300.17582657100
3.0159-3.31930.23671580.17022655100
3.3193-3.79930.17121570.15942620100
3.7993-4.78590.17121250.1342680100
4.78590.19661290.16292678100
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)
12.399-0.49340.54976.7001-1.47292.53490.1634-0.0062-0.07770.1774-0.17480.49560.0096-0.23390.00760.24120.0106-0.01590.3161-0.01670.2956-0.137418.507887.4012
21.81410.63670.37112.3631-0.31831.5979-0.00520.0392-0.0716-0.0664-0.01150.28250.1601-0.1710.01250.23320.005-0.02370.2111-0.01980.23696.257916.847292.4984
33.42360.34031.38951.69650.55131.89120.0973-0.334-0.28930.2148-0.1163-0.22550.1638-0.1071-0.01670.2460.0033-0.0270.19810.0170.171818.590714.4457101.3696
41.7054-0.11020.91462.033-0.45463.10770.2705-0.0829-0.1744-0.2234-0.16470.07690.4897-0.0495-0.09730.33460.0065-0.0080.2662-0.00710.255820.04737.7838101.2216
51.04390.12880.01931.91930.33440.98910.0660.2048-0.1386-0.1439-0.0456-0.20430.20730.199-0.01880.2510.04790.00090.2184-0.00310.19822.717813.62791.0109
61.91170.6549-0.45992.0979-0.30011.4017-0.02150.37410.3357-0.19390.0372-0.5842-0.36550.31170.0290.2626-0.02490.0190.27240.00310.302526.103426.348486.4736
70.4620.66470.38641.66280.07241.686-0.15460.45130.0871-0.07530.0096-0.0917-0.02440.09390.03340.20440.0097-0.01850.17920.00250.177621.085520.090883.8806
83.39940.78350.04343.6248-0.09382.6657-0.02950.38630.3375-0.32380.11640.3139-0.32880.15850.09150.2185-0.0445-0.02330.25410.03130.292528.656639.0931100.2548
93.1796-0.92710.09884.46550.03512.7741-0.00070.48980.2842-0.52790.12840.1375-0.25490.01360.07960.2664-0.0446-0.05460.20450.0420.284521.079236.050494.8647
102.65280.38190.2766.7065-1.67593.302-0.0199-0.06230.596-0.03050.15650.1954-0.2075-0.36620.08320.2509-0.01030.00080.2166-0.03350.316.419235.7694104.1847
112.04390.84410.56952.38010.04991.46490.1513-0.1371-0.02960.2932-0.04590.01780.0981-0.24090.03660.2727-0.0162-0.01740.2006-0.01070.174514.590116.2273105.4705
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 134 through 153 )
2X-RAY DIFFRACTION2chain 'A' and (resid 154 through 185 )
3X-RAY DIFFRACTION3chain 'A' and (resid 186 through 203 )
4X-RAY DIFFRACTION4chain 'A' and (resid 204 through 226 )
5X-RAY DIFFRACTION5chain 'A' and (resid 227 through 260 )
6X-RAY DIFFRACTION6chain 'A' and (resid 261 through 276 )
7X-RAY DIFFRACTION7chain 'A' and (resid 277 through 300 )
8X-RAY DIFFRACTION8chain 'E' and (resid -3 through 11 )
9X-RAY DIFFRACTION9chain 'E' and (resid 12 through 28 )
10X-RAY DIFFRACTION10chain 'E' and (resid 29 through 43 )
11X-RAY DIFFRACTION11chain 'E' and (resid 44 through 52 )

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