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- PDB-1cfz: HYDROGENASE MATURATING ENDOPEPTIDASE HYBD FROM E. COLI -

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Basic information

Entry
Database: PDB / ID: 1cfz
TitleHYDROGENASE MATURATING ENDOPEPTIDASE HYBD FROM E. COLI
ComponentsHYDROGENASE 2 MATURATION PROTEASE
KeywordsHYDROGENASE / MATURATION / METZINCINS / NICKEL / PROTEASE
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / enzyme activator activity / protein processing / endopeptidase activity / aspartic-type endopeptidase activity / metal ion binding
Similarity search - Function
Peptidase A31, hydrogenase expression/formation protein / 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 2 maturation protease
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.2 Å
AuthorsFritsche, E. / Paschos, A. / Beisel, H.-G. / Boeck, A. / Huber, R.
CitationJournal: J.Mol.Biol. / Year: 1999
Title: Crystal structure of the hydrogenase maturating endopeptidase HYBD from Escherichia coli.
Authors: Fritsche, E. / Paschos, A. / Beisel, H.G. / Bock, A. / Huber, R.
History
DepositionMar 23, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Mar 22, 2000Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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_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

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Assembly

Deposited unit
A: HYDROGENASE 2 MATURATION PROTEASE
B: HYDROGENASE 2 MATURATION PROTEASE
C: HYDROGENASE 2 MATURATION PROTEASE
D: HYDROGENASE 2 MATURATION PROTEASE
E: HYDROGENASE 2 MATURATION PROTEASE
F: HYDROGENASE 2 MATURATION PROTEASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,61612
Polymers104,9426
Non-polymers6746
Water4,936274
1
A: HYDROGENASE 2 MATURATION PROTEASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,6032
Polymers17,4901
Non-polymers1121
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: HYDROGENASE 2 MATURATION PROTEASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,6032
Polymers17,4901
Non-polymers1121
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: HYDROGENASE 2 MATURATION PROTEASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,6032
Polymers17,4901
Non-polymers1121
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: HYDROGENASE 2 MATURATION PROTEASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,6032
Polymers17,4901
Non-polymers1121
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: HYDROGENASE 2 MATURATION PROTEASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,6032
Polymers17,4901
Non-polymers1121
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: HYDROGENASE 2 MATURATION PROTEASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,6032
Polymers17,4901
Non-polymers1121
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)128.000, 128.000, 139.700
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number153
Space group name H-MP3212
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.992258, -0.060072, -0.108697), (-0.065483, 0.99675, 0.046907), (0.105525, 0.053662, -0.992968)61.14209, -37.3908, 90.79066
3given(-0.491752, 0.870714, -0.006029), (-0.870386, -0.49174, -0.024903), (-0.024648, -0.006999, 0.999672)62.87239, 40.21555, 23.75972
4given(0.475165, 0.868937, -0.138441), (0.866365, -0.489517, -0.098913), (-0.153719, -0.07294, -0.985419)3.66341, 78.60965, 70.21279
5given(0.445933, 0.894177, -0.039894), (0.893091, -0.447466, -0.046499), (-0.059429, -0.014894, -0.998121)1.82044, 1.83188, 69.17489
6given(-0.993203, -0.078888, 0.085585), (-0.079894, 0.996768, -0.008391), (-0.084647, -0.015171, -0.996295)67.97655, 40.30783, 87.49628

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Components

#1: Protein
HYDROGENASE 2 MATURATION PROTEASE


Mass: 17490.318 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli)
References: UniProt: P37182, Hydrolases; Acting on peptide bonds (peptidases)
#2: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cd
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 274 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsMETAL ION WAS MODELED AS A CADMIUM ION

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.15 Å3/Da / Density % sol: 60.91 %
Crystal growpH: 6.5 / Details: pH 6.50
Crystal
*PLUS
Density % sol: 61 %
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 6.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
125 mg/mlprotein1drop
210 mMMES-NaOH1drop
3100 mMMES-NaOH1reservoir
40.9 Mammonium sulfate1reservoir
51 mM1reservoirCdSO4

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.099
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.099 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. obs: 62671 / % possible obs: 94.6 % / Observed criterion σ(I): 2 / Redundancy: 2 % / Rsym value: 10.3
Reflection
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 20 Å / % possible obs: 94.6 % / Observed criterion σ(I): 2 / Redundancy: 2 % / Num. measured all: 125012 / Rmerge(I) obs: 0.103
Reflection shell
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 2.27 Å / % possible obs: 90.3 % / Rmerge(I) obs: 0.267

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Processing

SoftwareName: REFMAC / Classification: refinement
RefinementMethod to determine structure: SIRAS / Resolution: 2.2→15 Å / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.259 -10 %
Rwork0.224 --
obs-62539 95 %
Refinement stepCycle: LAST / Resolution: 2.2→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7350 0 6 274 7630
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.011
X-RAY DIFFRACTIONp_angle_d0.021
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Refinement
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 15 Å / Num. reflection Rfree: 6246 / Rfactor obs: 0.224
Solvent computation
*PLUS
Displacement parameters
*PLUS

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