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- PDB-1gxu: Hydrogenase Maturation Protein HypF "acylphosphatase-like" N-term... -

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Basic information

Entry
Database: PDB / ID: 1gxu
TitleHydrogenase Maturation Protein HypF "acylphosphatase-like" N-terminal domain (HypF-ACP) in complex with a substrate. Crystal grown in the presence of carbamoylphosphate
ComponentsHYDROGENASE MATURATION PROTEIN HYPF
KeywordsPHOSPHATASE / ACYLPHOSPHATASES / HYDROGENASE MATURATIONS / FIBRIL FORMATION / ZINC-FINGER
Function / homology
Function and homology information


Ligases; Forming carbon-sulfur bonds / carboxyl- or carbamoyltransferase activity / ATPase complex / ligase activity / protein maturation / double-stranded RNA binding / protein-containing complex assembly / zinc ion binding
Similarity search - Function
Carbamoyltransferase, HypF-type / Zinc finger, HypF-type / HypF, Kae1-like domain / : / HypF finger / HypF Kae1-like domain / Carbamoyltransferase, Kae1-like Domain, second subdomain / : / Threonylcarbamoyl-AMP synthase-like domain / Telomere recombination ...Carbamoyltransferase, HypF-type / Zinc finger, HypF-type / HypF, Kae1-like domain / : / HypF finger / HypF Kae1-like domain / Carbamoyltransferase, Kae1-like Domain, second subdomain / : / Threonylcarbamoyl-AMP synthase-like domain / Telomere recombination / YrdC-like domain profile. / Acylphosphatase signature 1. / Acylphosphatase, conserved site / Acylphosphatase / Acylphosphatase-like domain / Acylphosphatase-like domain profile. / DHBP synthase RibB-like alpha/beta domain superfamily / Acylphosphatase-like domain superfamily / Alpha-Beta Plaits - #100 / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
DIHYDROGENPHOSPHATE ION / Carbamoyltransferase HypF
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.27 Å
AuthorsRosano, C. / Zuccotti, S. / Stefani, M. / Bucciantini, M. / Ramponi, G. / Bolognesi, M.
CitationJournal: J.Mol.Biol. / Year: 2002
Title: Crystal Structure and Anion Binding in the Prokaryotic Hydrogenase Maturation Factor Hypf Acylphosphatase-Like Domain
Authors: Rosano, C. / Zuccotti, S. / Bucciantini, M. / Stefani, M. / Ramponi, G. / Bolognesi, M.
History
DepositionApr 11, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 12, 2002Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_special_symmetry
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HYDROGENASE MATURATION PROTEIN HYPF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,5022
Polymers10,4051
Non-polymers971
Water1,964109
1
A: HYDROGENASE MATURATION PROTEIN HYPF
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)63,01112
Polymers62,4296
Non-polymers5826
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation4_556y,x,-z+11
crystal symmetry operation5_556x-y,-y,-z+11
crystal symmetry operation6_556-x,-x+y,-z+11
MethodPQS
Unit cell
Length a, b, c (Å)57.994, 57.994, 156.414
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-2009-

HOH

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Components

#1: Protein HYDROGENASE MATURATION PROTEIN HYPF


Mass: 10404.901 Da / Num. of mol.: 1 / Fragment: ACYLPHOSPHATASE-LIKE DOMAIN, RESIDUES 1-91 / Source method: obtained synthetically / Source: (synth.) ESCHERICHIA COLI (E. coli) / References: UniProt: P30131
#2: Chemical ChemComp-2HP / DIHYDROGENPHOSPHATE ION


Mass: 96.987 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H2O4P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 109 / 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: 2.51 Å3/Da / Density % sol: 50.9 %
Crystal growpH: 8.5 / Details: pH 8.50
Crystal grow
*PLUS
pH: 5.5 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
130.0 %(w/v)PEG40001reservoir
2100 mMsodium acetate1reservoirpH5.5
38.0 mg/mlprotein1drop
410.0 %(v/v)glycerol1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.27→30 Å / Num. obs: 27134 / % possible obs: 99.9 % / Observed criterion σ(I): 3 / Redundancy: 10.8 % / Rmerge(I) obs: 0.027 / Net I/σ(I): 35.7
Reflection
*PLUS
Lowest resolution: 30 Å / Num. measured all: 292257
Reflection shell
*PLUS
Mean I/σ(I) obs: 35.7

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Processing

Software
NameClassification
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
CCP4phasing
RefinementMethod to determine structure: OTHER / Resolution: 1.27→10 Å / SU B: 0.595 / SU ML: 0.029 / ESU R Free: 0.038
Details: IN THE ACTIVE SITE, WE ARE ABLE TO SEE ONLY THE PHOSPHATE MOIETY OF CARBAMOYLPHOSPHATE
RfactorNum. reflection% reflectionSelection details
Rfree0.161 1352 5 %RANDOM
Rwork0.131 ---
obs0.133 25674 99.9 %-
Displacement parametersBiso mean: 17.3 Å2
Baniso -1Baniso -2Baniso -3
1-0.62 Å20 Å20.31 Å2
2--0.62 Å20 Å2
3----0.93 Å2
Refinement stepCycle: LAST / Resolution: 1.27→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms710 0 5 109 824
Refinement
*PLUS
Lowest resolution: 10 Å / Rfactor Rfree: 0.1613 / Rfactor Rwork: 0.1315
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.019
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg1.881
X-RAY DIFFRACTIONp_plane_restr0.019
LS refinement shell
*PLUS
Highest resolution: 1.271 Å / Lowest resolution: 1.303 Å / Rfactor Rfree: 0.203 / Rfactor Rwork: 0.212 / Num. reflection Rwork: 1856 / Total num. of bins used: 20

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