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- PDB-2hf9: Crystal structure of HypB from Methanocaldococcus jannaschii in t... -

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Basic information

Entry
Database: PDB / ID: 2hf9
TitleCrystal structure of HypB from Methanocaldococcus jannaschii in the triphosphate form
ComponentsProbable hydrogenase nickel incorporation protein hypB
KeywordsHYDROLASE / Metal Binding Protein / alpha and beta protein / P-loop containing nucleoside triphosphate hydrolase
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 / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE / Probable hydrogenase maturation factor HypB
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / MAD / Resolution: 1.9 Å
AuthorsGasper, R. / Scrima, A. / Wittinghofer, A.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: Structural insights into HypB, a GTP-binding protein that regulates metal binding.
Authors: Gasper, R. / Scrima, A. / Wittinghofer, A.
History
DepositionJun 23, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 4, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 30, 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_ref_seq_dif / 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.ptnr1_symmetry / _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.ptnr3_symmetry / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Probable hydrogenase nickel incorporation protein hypB
B: Probable hydrogenase nickel incorporation protein hypB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,7668
Polymers49,5082
Non-polymers1,2586
Water3,135174
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4830 Å2
ΔGint-41 kcal/mol
Surface area16510 Å2
MethodPISA
2
A: Probable hydrogenase nickel incorporation protein hypB
hetero molecules

B: Probable hydrogenase nickel incorporation protein hypB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,7668
Polymers49,5082
Non-polymers1,2586
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_455x-1/2,-y+1/2,-z1
Buried area2330 Å2
ΔGint-113 kcal/mol
Surface area19210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.463, 68.107, 155.840
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Detailsbiological unit is composed of chain A and B

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Components

#1: Protein Probable hydrogenase nickel incorporation protein hypB


Mass: 24753.955 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Gene: hypB / Plasmid: pGex4T3 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta DE3 / References: UniProt: Q57884
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-GSP / 5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE


Mass: 539.246 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 174 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.33 Å3/Da / Density % sol: 47.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 150 mM maleic acid disodium salt, 42.5 mM HCl, 20% PEG3350, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9758 Å
DetectorType: ADSC / Detector: CCD / Date: Feb 8, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9758 Å / Relative weight: 1
ReflectionAv σ(I) over netI: 20.54 / Number: 194237 / Rmerge(I) obs: 0.048 / D res high: 2.1 Å / Num. obs: 51141 / % possible obs: 98.6
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obs
2.12.293.110.084
2.22.398.810.092
2.32.499.210.087
2.42.599.410.079
2.72.899.610.053
2.52.699.610.066
2.62.799.810.06
2.82.999.810.048
2.9399.910.046
33.599.810.039
3.5499.910.038
4599.910.051
5699.810.05
ReflectionResolution: 2.1→20 Å / Num. all: 51141 / Num. obs: 51141 / % possible obs: 98.6 % / Observed criterion σ(F): 3 / Redundancy: 6.5 % / Biso Wilson estimate: 24.484 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 20.54
Reflection shellResolution: 2.1→2.2 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.084 / Mean I/σ(I) obs: 9.3 / Num. measured obs: 13086 / Num. unique all: 6342 / % possible all: 93.1

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Phasing

PhasingMethod: MAD
Phasing MADD res high: 2.1 Å / D res low: 20 Å / FOM : 0.39 / Reflection: 27579
Phasing MAD set site
IDAtom type symbolB isoFract xFract yFract zOccupancy
1Se16.9620.0610.1320.2480.93
2Se16.8310.210.4130.1960.902
3Se20.5450.8840.590.2010.998
4Se17.2630.7740.2770.1860.883
5Se15.3560.8180.1920.1330.87
6Se21.0620.9870.1430.1070.849
7Se14.0140.2410.4460.1340.785
8Se23.4120.280.1180.1640.9
9Se20.5930.7790.5250.1050.71
10Se26.6050.120.4640.0860.863
11Se22.1320.3610.0540.0270.553
12Se23.330.0510.2750.0580.392
Phasing MAD shell
Resolution (Å)FOM Reflection
7.31-200.431466
4.7-7.310.422343
3.7-4.70.452927
3.15-3.70.473423
2.79-3.150.453837
2.52-2.790.424209
2.33-2.520.334539
2.17-2.330.264835
Phasing dmFOM : 0.72 / FOM acentric: 0.74 / FOM centric: 0.62 / Reflection: 27579 / Reflection acentric: 24064 / Reflection centric: 3515
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
6-19.9290.880.920.791278890388
3.8-60.90.920.7837753096679
3-3.80.860.890.746584035623
2.6-30.770.80.646324099533
2.3-2.60.640.660.4981937362831
2.1-2.30.50.510.3650434582461

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
SOLVE2.06phasing
RESOLVE2.06phasing
REFMACrefmac_5.2.0005refinement
PDB_EXTRACT2data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry: 2Hf8

2hf8


Resolution: 1.9→19.96 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.91 / SU B: 3.336 / SU ML: 0.101 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.181 / ESU R Free: 0.153 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.241 3723 10 %RANDOM
Rwork0.217 ---
all0.22 37222 --
obs-37222 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.316 Å2
Baniso -1Baniso -2Baniso -3
1-0.8 Å20 Å20 Å2
2---0.28 Å20 Å2
3----0.53 Å2
Refinement stepCycle: LAST / Resolution: 1.9→19.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3246 0 68 174 3488
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0223352
X-RAY DIFFRACTIONr_angle_refined_deg1.1042.0114522
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2695418
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.36826.324136
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.06915662
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.761510
X-RAY DIFFRACTIONr_chiral_restr0.0730.2536
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022360
X-RAY DIFFRACTIONr_nbd_refined0.1850.21537
X-RAY DIFFRACTIONr_nbtor_refined0.2930.22273
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1230.2258
X-RAY DIFFRACTIONr_metal_ion_refined0.1190.23
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1610.232
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0820.29
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.1620.22
X-RAY DIFFRACTIONr_mcbond_it0.4391.52158
X-RAY DIFFRACTIONr_mcangle_it0.73323346
X-RAY DIFFRACTIONr_scbond_it1.03231332
X-RAY DIFFRACTIONr_scangle_it1.7324.51176
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.298 265 -
Rwork0.242 2381 -
obs-2646 100 %

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