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- PDB-2e85: Crystal Structure of the Hydrogenase 3 Maturation protease -

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Basic information

Entry
Database: PDB / ID: 2.0E+85
TitleCrystal Structure of the Hydrogenase 3 Maturation protease
ComponentsHydrogenase 3 maturation protease
KeywordsHYDROLASE / hydrogenase / maturation / protease / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


HycI peptidase / enzyme activator activity / protein processing / endopeptidase activity / aspartic-type endopeptidase activity / metal ion binding
Similarity search - Function
Peptidase A31, hydrogenase maturation protease HycI / Hydrogenase maturation protease / HybD-like / Peptidase A31 family / Peptidase HybD-like domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Hydrogenase 3 maturation protease
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.7 Å
AuthorsTanaka, T. / Kumarevel, T.S. / Shinkai, A. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2009
Title: Crystal structure of hydrogenase maturating endopeptidase HycI from Escherichia coli
Authors: Kumarevel, T. / Tanaka, T. / Bessho, Y. / Shinkai, A. / Yokoyama, S.
History
DepositionJan 18, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 22, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / 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.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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hydrogenase 3 maturation protease
B: Hydrogenase 3 maturation protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,7688
Polymers34,5272
Non-polymers2406
Water4,954275
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2270 Å2
ΔGint-66 kcal/mol
Surface area14000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.425, 54.984, 67.964
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-1066-

HOH

DetailsTHE DEPOSITOR DID NOT CHARACTERIZED THE PROTEIN COMPLETELY BY BIOCHEMICALLY. MAY BE A DIMER BASED ON THE CRYSTAL PACKING

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Components

#1: Protein Hydrogenase 3 maturation protease


Mass: 17263.600 Da / Num. of mol.: 2 / Mutation: M1V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: pCA24N / Production host: cell-free synthesis (others)
References: UniProt: P0AEV9, Hydrolases; Acting on peptide bonds (peptidases)
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 275 / 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: 2.36 Å3/Da / Density % sol: 47.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2M CaCl2, 0.1M Sodium Hepes, 28% PEG 400, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 0.97921, 0.97955, 1.0000
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 18, 2006
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979211
20.979551
311
ReflectionResolution: 1.7→50 Å / Num. all: 36372 / Num. obs: 36372 / % possible obs: 98.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 6.5 % / Biso Wilson estimate: 13.5 Å2 / Rmerge(I) obs: 0.084 / Net I/σ(I): 19.54
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.231 / Mean I/σ(I) obs: 5.84 / Num. unique all: 3529 / % possible all: 97.7

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Processing

Software
NameVersionClassification
CNS1.1refinement
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.7→20 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1580148.08 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.258 1790 5 %RANDOM
Rwork0.248 ---
obs0.248 35885 97.7 %-
all-36372 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 57.9681 Å2 / ksol: 0.44607 e/Å3
Displacement parametersBiso mean: 14.8 Å2
Baniso -1Baniso -2Baniso -3
1-1.85 Å20 Å20 Å2
2---0.46 Å20 Å2
3----1.38 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a-0.04 Å
Refinement stepCycle: LAST / Resolution: 1.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2362 0 6 284 2652
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.014
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d25.6
X-RAY DIFFRACTIONc_improper_angle_d1.62
X-RAY DIFFRACTIONc_mcbond_it1.181.5
X-RAY DIFFRACTIONc_mcangle_it1.582
X-RAY DIFFRACTIONc_scbond_it2.552
X-RAY DIFFRACTIONc_scangle_it3.322.5
LS refinement shellResolution: 1.7→1.81 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.253 276 4.8 %
Rwork0.243 5461 -
obs--95.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3dna-rna_rep.paramdna-rna_rep.param
X-RAY DIFFRACTION4ion.paramion.param

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