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- PDB-4lps: Crystal structure of HypB from Helicobacter pylori in complex wit... -

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Basic information

Entry
Database: PDB / ID: 4lps
TitleCrystal structure of HypB from Helicobacter pylori in complex with nickel
ComponentsHydrogenase/urease nickel incorporation protein HypB
KeywordsMETAL BINDING PROTEIN / Hydrogenase nickel incorporation GTPase
Function / homology
Function and homology information


nickel cation binding / protein maturation / GTPase activity / GTP binding / zinc ion binding
Similarity search - Function
Hydrogenase maturation factor HypB / CobW/HypB/UreG, nucleotide-binding domain / CobW/HypB/UreG, nucleotide-binding domain / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / MALONATE ION / NICKEL (II) ION / PHOSPHATE ION / Hydrogenase/urease maturation factor HypB
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsLebrette, H. / Sydor, A.M. / Ariyakumaran, R. / Zamble, D.B. / Cavazza, C.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Relationship between Ni(II) and Zn(II) Coordination and Nucleotide Binding by the Helicobacter pylori [NiFe]-Hydrogenase and Urease Maturation Factor HypB.
Authors: Sydor, A.M. / Lebrette, H. / Ariyakumaran, R. / Cavazza, C. / Zamble, D.B.
History
DepositionJul 16, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 26, 2014Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_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 / _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: Hydrogenase/urease nickel incorporation protein HypB
B: Hydrogenase/urease nickel incorporation protein HypB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,11222
Polymers54,6932
Non-polymers2,41920
Water6,035335
1
A: Hydrogenase/urease nickel incorporation protein HypB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,54311
Polymers27,3461
Non-polymers1,19710
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Hydrogenase/urease nickel incorporation protein HypB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,56911
Polymers27,3461
Non-polymers1,22310
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.820, 50.160, 53.680
Angle α, β, γ (deg.)102.16, 99.05, 90.65
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Hydrogenase/urease nickel incorporation protein HypB


Mass: 27346.443 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Strain: ATCC 700392 / 26695 / Gene: hypB, HP_0900 / Production host: Escherichia coli (E. coli) / References: UniProt: O25560

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Non-polymers , 7 types, 355 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#4: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-MLI / MALONATE ION / Malonic acid


Mass: 102.046 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H2O4
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 335 / Source method: isolated from a natural source / Formula: H2O

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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: 2.37 Å3/Da / Density % sol: 48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 1.0 M Malonate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.97969 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 11, 2013
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97969 Å / Relative weight: 1
ReflectionResolution: 2→40.152 Å / Num. obs: 33146 / % possible obs: 97.7 % / Observed criterion σ(I): -3 / Rsym value: 0.099
Reflection shellResolution: 2→2.1 Å / Redundancy: 3.84 % / Mean I/σ(I) obs: 3.47 / Rsym value: 0.516 / % possible all: 96.5

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Processing

Software
NameVersionClassification
MXCUBEdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2HF9

2hf9


Resolution: 2→40.15 Å / σ(F): 1.99 / Phase error: 21.16 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.1964 1734 5.23 %RANDOM
Rwork0.1704 ---
obs0.1721 33146 97.85 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→40.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3380 0 147 335 3862
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043592
X-RAY DIFFRACTIONf_angle_d1.0934826
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.05890.27831370.23332596X-RAY DIFFRACTION92
2.0589-2.12540.24021370.20882594X-RAY DIFFRACTION92
2.1254-2.20130.22871370.19162608X-RAY DIFFRACTION93
2.2013-2.28950.22341370.18312602X-RAY DIFFRACTION92
2.2895-2.39360.21331390.18162638X-RAY DIFFRACTION93
2.3936-2.51980.2321380.18552630X-RAY DIFFRACTION93
2.5198-2.67770.23071370.17522603X-RAY DIFFRACTION93
2.6777-2.88430.21271380.17552614X-RAY DIFFRACTION93
2.8843-3.17450.18451400.16382659X-RAY DIFFRACTION93
3.1745-3.63360.16591390.14882640X-RAY DIFFRACTION94
3.6336-4.57680.16631390.13532640X-RAY DIFFRACTION94
4.5768-38.97110.17481400.1752659X-RAY DIFFRACTION94
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)
17.6621-1.19742.68758.3887-3.10228.4312-0.08080.0406-0.3468-0.17160.1641-0.1795-0.0393-0.0976-0.07240.0692-0.0178-0.0490.1748-0.03350.098637.7528-10.5468-4.3566
23.7682-0.094-0.65031.08140.24891.69440.05070.26160.338-0.1728-0.0402-0.053-0.1649-0.0739-0.02010.15820.0003-0.04860.1160.01050.114620.46320.7643-5.1821
32.88920.00770.41610.3747-0.13922.63770.12520.1635-0.2045-0.1864-0.0886-0.04820.2772-0.1562-0.02910.1825-0.0348-0.04380.2325-0.01790.086718.5873-10.26-8.7726
42.6675-0.54861.15930.9201-0.79532.4564-0.0550.3716-0.1249-0.1899-0.03490.01950.0136-0.06370.00950.2028-0.0214-0.05180.2116-0.04480.091722.0432-10.9533-10.831
52.1815-0.5219-0.53771.33230.35320.2786-0.0098-0.09240.09940.0944-0.0415-0.1137-0.1080.07020.04680.1355-0.0142-0.06260.1369-0.00780.088921.9258-4.7884.2168
67.4758-0.15873.5332.7080.98785.5044-0.2071-0.62550.20450.35020.081-0.013-0.1864-0.14220.12750.2207-0.0064-0.03040.1322-0.03970.088312.32063.067115.7145
73.86040.6023-1.06471.11860.65861.48990.1993-0.11510.57420.0809-0.0018-0.202-0.26220.0832-0.15130.1969-0.0452-0.00810.1248-0.00710.241624.58316.20372.7621
83.3892-0.0949-3.12793.7215-0.47822.97270.0395-0.2165-0.10890.0057-0.1292-0.1338-0.06340.08710.12020.1532-0.0124-0.04630.1334-0.02190.099311.8784-36.946217.1668
91.04480.0429-0.12952.8555-1.21541.6879-0.0104-0.19090.04030.30020.04810.1224-0.1496-0.1024-0.03980.17-0.0133-0.02550.1664-0.02470.07192.0009-19.787518.8853
105.3488-2.4285-6.33051.59432.46578.04470.5298-0.39120.9417-0.17920.0599-0.4482-1.43330.487-0.58660.5141-0.0601-0.03080.3374-0.10420.27229.7907-12.597725.3201
110.7476-0.3308-0.0561.9012-0.70790.9646-0.0419-0.03740.00010.07820.0013-0.017-0.018-0.03960.05050.1429-0.0319-0.03950.1329-0.03850.07177.2706-20.259912.0889
120.8206-0.50150.03052.3914-1.30341.95780.01190.0992-0.1696-0.1740.11920.32760.2063-0.2951-0.1120.1349-0.0533-0.05850.1846-0.01590.1586-4.1345-22.67916.486
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 28:43 )
2X-RAY DIFFRACTION2CHAIN A AND (RESID 44:73 )
3X-RAY DIFFRACTION3CHAIN A AND (RESID 74:84 )
4X-RAY DIFFRACTION4CHAIN A AND (RESID 85:123 )
5X-RAY DIFFRACTION5CHAIN A AND (RESID 124:183 )
6X-RAY DIFFRACTION6CHAIN A AND (RESID 184:204 )
7X-RAY DIFFRACTION7CHAIN A AND (RESID 205:242 )
8X-RAY DIFFRACTION8CHAIN B AND (RESID 28:43 )
9X-RAY DIFFRACTION9CHAIN B AND (RESID 44:80 )
10X-RAY DIFFRACTION10CHAIN B AND (RESID 81:93 )
11X-RAY DIFFRACTION11CHAIN B AND (RESID 94:193 )
12X-RAY DIFFRACTION12CHAIN B AND (RESID 194:242 )

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