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- PDB-4xdd: Apo [FeFe]-Hydrogenase CpI -

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Basic information

Entry
Database: PDB / ID: 4xdd
TitleApo [FeFe]-Hydrogenase CpI
ComponentsIron hydrogenase 1
KeywordsOXIDOREDUCTASE / CpI / FeFe-Hydrogenase
Function / homology
Function and homology information


ferredoxin hydrogenase / ferredoxin hydrogenase activity / 4 iron, 4 sulfur cluster binding / iron ion binding
Similarity search - Function
Ubiquitin-like (UB roll) - #740 / : / Iron hydrogenase 1-like, iron-sulfur centre-binding domain / Iron hydrogenase, small subunit superfamily / Iron hydrogenase, subset / Iron hydrogenase, small subunit / : / Iron hydrogenase small subunit / Iron hydrogenase small subunit / Iron hydrogenase, large subunit, C-terminal ...Ubiquitin-like (UB roll) - #740 / : / Iron hydrogenase 1-like, iron-sulfur centre-binding domain / Iron hydrogenase, small subunit superfamily / Iron hydrogenase, subset / Iron hydrogenase, small subunit / : / Iron hydrogenase small subunit / Iron hydrogenase small subunit / Iron hydrogenase, large subunit, C-terminal / Iron hydrogenase / Iron only hydrogenase large subunit, C-terminal domain / Alpha-Beta Plaits - #20 / 2Fe-2S iron-sulfur cluster binding domain / NADH:ubiquinone oxidoreductase, subunit G, iron-sulphur binding / His(Cys)3-ligated-type [4Fe-4S] domain profile. / 4Fe-4S dicluster domain / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. / 2Fe-2S ferredoxin-type iron-sulfur binding domain / 2Fe-2S ferredoxin-like superfamily / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type, iron-sulphur binding domain / Ubiquitin-like (UB roll) / Alpha-Beta Plaits / Roll / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
FE2/S2 (INORGANIC) CLUSTER / IRON/SULFUR CLUSTER / Iron hydrogenase 1
Similarity search - Component
Biological speciesClostridium pasteurianum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.599 Å
AuthorsEsselborn, J. / Hofmann, E. / Kurisu, G. / Happe, T.
CitationJournal: Chem Sci / Year: 2016
Title: A structural view of synthetic cofactor integration into [FeFe]-hydrogenases.
Authors: Esselborn, J. / Muraki, N. / Klein, K. / Engelbrecht, V. / Metzler-Nolte, N. / Apfel, U.P. / Hofmann, E. / Kurisu, G. / Happe, T.
History
DepositionDec 19, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Nov 11, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 11, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Jan 10, 2024Group: 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
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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Iron hydrogenase 1
B: Iron hydrogenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,64523
Polymers129,9652
Non-polymers3,68021
Water25,2211400
1
A: Iron hydrogenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,77611
Polymers64,9821
Non-polymers1,79410
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Iron hydrogenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,86812
Polymers64,9821
Non-polymers1,88611
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)90.057, 71.807, 103.308
Angle α, β, γ (deg.)90.00, 97.93, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.774151, 0.585773, 0.239917), (0.584472, -0.80701, 0.084427), (0.243071, 0.074866, -0.967115)-19.21785, 43.46664, 37.98365

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Iron hydrogenase 1 / CpI / Fe-only hydrogenase / [Fe] hydrogenase


Mass: 64982.293 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium pasteurianum (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P29166, ferredoxin hydrogenase

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Non-polymers , 6 types, 1421 molecules

#2: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Fe4S4
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe2S2
#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1400 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.55 Å3/Da / Density % sol: 51.68 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: PEG4000, MgCl / PH range: 7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: May 22, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.599→50 Å / Num. obs: 172056 / % possible obs: 99.7 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.052 / Net I/σ(I): 36.8
Reflection shellResolution: 1.599→1.63 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 3.2 / % possible all: 99.5

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3C8Y

3c8y


Resolution: 1.599→38.963 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 17.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1658 8589 5.01 %RANDOM
Rwork0.1438 ---
obs0.1449 171439 99.59 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.599→38.963 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9139 0 0 1400 10539
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0069372
X-RAY DIFFRACTIONf_angle_d0.95212621
X-RAY DIFFRACTIONf_dihedral_angle_d13.4953487
X-RAY DIFFRACTIONf_chiral_restr0.0361373
X-RAY DIFFRACTIONf_plane_restr0.0041629
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5995-1.61770.27212680.25265261X-RAY DIFFRACTION97
1.6177-1.63670.27822870.24275435X-RAY DIFFRACTION100
1.6367-1.65670.26552980.22725368X-RAY DIFFRACTION100
1.6567-1.67760.22362510.22125445X-RAY DIFFRACTION100
1.6776-1.69970.25042580.21215451X-RAY DIFFRACTION100
1.6997-1.7230.24342660.20285387X-RAY DIFFRACTION100
1.723-1.74760.2262930.19225448X-RAY DIFFRACTION100
1.7476-1.77370.20262620.1855398X-RAY DIFFRACTION100
1.7737-1.80140.21022870.17925442X-RAY DIFFRACTION100
1.8014-1.83090.19792690.17255393X-RAY DIFFRACTION100
1.8309-1.86250.1913010.16475404X-RAY DIFFRACTION100
1.8625-1.89640.18382990.16085432X-RAY DIFFRACTION100
1.8964-1.93280.19993020.15985397X-RAY DIFFRACTION100
1.9328-1.97230.19392920.15445427X-RAY DIFFRACTION100
1.9723-2.01520.17122760.14755435X-RAY DIFFRACTION100
2.0152-2.06210.16142850.14545504X-RAY DIFFRACTION100
2.0621-2.11360.16362990.14225388X-RAY DIFFRACTION100
2.1136-2.17080.1642900.13925440X-RAY DIFFRACTION100
2.1708-2.23460.17833010.14065410X-RAY DIFFRACTION100
2.2346-2.30670.16623010.13235431X-RAY DIFFRACTION100
2.3067-2.38920.15812740.13285485X-RAY DIFFRACTION100
2.3892-2.48480.16423020.14015406X-RAY DIFFRACTION100
2.4848-2.59790.17042870.13945454X-RAY DIFFRACTION100
2.5979-2.73480.15742940.1425476X-RAY DIFFRACTION100
2.7348-2.90610.18782880.14635446X-RAY DIFFRACTION100
2.9061-3.13040.16632710.14475494X-RAY DIFFRACTION100
3.1304-3.44530.15673170.13815435X-RAY DIFFRACTION100
3.4453-3.94340.14642910.12485502X-RAY DIFFRACTION100
3.9434-4.96670.13082820.1155478X-RAY DIFFRACTION99
4.9667-38.97450.14762980.14165378X-RAY DIFFRACTION95

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