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- PDB-1cc1: CRYSTAL STRUCTURE OF A REDUCED, ACTIVE FORM OF THE NI-FE-SE HYDRO... -

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Basic information

Entry
Database: PDB / ID: 1cc1
TitleCRYSTAL STRUCTURE OF A REDUCED, ACTIVE FORM OF THE NI-FE-SE HYDROGENASE FROM DESULFOMICROBIUM BACULATUM
Components
  • HYDROGENASE (LARGE SUBUNIT)
  • HYDROGENASE (SMALL SUBUNIT)
KeywordsOXIDOREDUCTASE / NI-FE-SE HYDROGENASE
Function / homology
Function and homology information


hydrogenase (acceptor) / [Ni-Fe] hydrogenase complex / ferredoxin hydrogenase complex / hydrogenase (acceptor) activity / ferredoxin hydrogenase activity / anaerobic respiration / nickel cation binding / 4 iron, 4 sulfur cluster binding / periplasmic space / electron transfer activity ...hydrogenase (acceptor) / [Ni-Fe] hydrogenase complex / ferredoxin hydrogenase complex / hydrogenase (acceptor) activity / ferredoxin hydrogenase activity / anaerobic respiration / nickel cation binding / 4 iron, 4 sulfur cluster binding / periplasmic space / electron transfer activity / membrane / metal ion binding
Similarity search - Function
Cytochrome-c3 Hydrogenase; Chain A, domain 2 / Cytochrome-c3 hydrogenase, C-terminal domain / NADH:ubiquinone oxidoreductase-like, 20kDa subunit / Cytochrome-c3 Hydrogenase; chain B / Cytochrome-c3 Hydrogenase, chain B / [NiFe]-hydrogenase, small subunit / Cytochrome-c3 hydrogenase, C-terminal / [NiFe]-hydrogenase, small subunit, C-terminal domain superfamily / NiFe/NiFeSe hydrogenase small subunit C-terminal / Nickel-dependent hydrogenases large subunit signature 2. ...Cytochrome-c3 Hydrogenase; Chain A, domain 2 / Cytochrome-c3 hydrogenase, C-terminal domain / NADH:ubiquinone oxidoreductase-like, 20kDa subunit / Cytochrome-c3 Hydrogenase; chain B / Cytochrome-c3 Hydrogenase, chain B / [NiFe]-hydrogenase, small subunit / Cytochrome-c3 hydrogenase, C-terminal / [NiFe]-hydrogenase, small subunit, C-terminal domain superfamily / NiFe/NiFeSe hydrogenase small subunit C-terminal / Nickel-dependent hydrogenases large subunit signature 2. / Nickel-dependent hydrogenases large subunit signature 1. / [NiFe]-hydrogenase, small subunit, N-terminal domain superfamily / Nickel-dependent hydrogenase, large subunit, nickel binding site / Nickel-dependent hydrogenase, large subunit / Nickel-dependent hydrogenase / Twin-arginine translocation pathway, signal sequence, bacterial/archaeal / NADH:ubiquinone oxidoreductase-like, 20kDa subunit / NADH ubiquinone oxidoreductase, 20 Kd subunit / [NiFe]-hydrogenase, large subunit / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / Few Secondary Structures / Irregular / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
CARBONMONOXIDE-(DICYANO) IRON / : / HYDROSULFURIC ACID / NICKEL (II) ION / IRON/SULFUR CLUSTER / Periplasmic [NiFeSe] hydrogenase small subunit / Periplasmic [NiFeSe] hydrogenase large subunit
Similarity search - Component
Biological speciesDesulfomicrobium baculatum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsGarcin, E. / Vernede, X. / Hatchikian, E.C. / Volbeda, A. / Frey, M. / Fontecilla-Camps, J.C.
Citation
Journal: Structure Fold.Des. / Year: 1999
Title: The crystal structure of a reduced [NiFeSe] hydrogenase provides an image of the activated catalytic center
Authors: Garcin, E. / Vernede, X. / Hatchikian, E.C. / Volbeda, A. / Frey, M. / Fontecilla-Camps, J.C.
#1: Journal: J.Am.Chem.Soc. / Year: 1996
Title: Structure of the [NiFe] Hydrogenase Active Site: Evidence for Biologically Uncommon Fe Ligands
Authors: Volbeda, A. / Garcin, E. / Piras, C. / De Lacey, A.L. / Fernandez, V.M. / Hatchikian, E.C. / Frey, M. / Fontecilla-Camps, J.C.
History
DepositionMar 3, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Jun 1, 1999Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 19, 2014Group: Atomic model / Structure summary
Revision 1.4Aug 6, 2014Group: Derived calculations / Structure summary
Revision 1.5Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.6Apr 11, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_beamline
Revision 1.7Nov 20, 2019Group: Database references / Derived calculations
Category: pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif
Item: _struct_ref_seq_dif.details
Revision 1.8Aug 9, 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_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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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

Downloads & links

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Assembly

Deposited unit
S: HYDROGENASE (SMALL SUBUNIT)
L: HYDROGENASE (LARGE SUBUNIT)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,4459
Polymers86,1062
Non-polymers1,3397
Water5,747319
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8200 Å2
ΔGint-124 kcal/mol
Surface area23560 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)110.390, 63.700, 99.580
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 2 molecules SL

#1: Protein HYDROGENASE (SMALL SUBUNIT) / CYTOCHROME C3 HYDROGENASE


Mass: 30888.158 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Desulfomicrobium baculatum (bacteria) / Cellular location: PERIPLASM / Strain: WILD TYPE / References: UniProt: P13063, 1.18.99.1
#2: Protein HYDROGENASE (LARGE SUBUNIT) / CYTOCHROME C3 HYDROGENASE


Mass: 55217.805 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: COMPLEXED WITH IRON/SULFUR CLUSTER, CARBONMONOXIDE-(DICYANO) IRON, HYDROSULFURIC ACID
Source: (natural) Desulfomicrobium baculatum (bacteria) / Cellular location: PERIPLASM / Strain: WILD TYPE / References: UniProt: P13065, 1.18.99.1

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Non-polymers , 6 types, 326 molecules

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


Mass: 351.640 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe4S4
#4: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#5: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#6: Chemical ChemComp-FCO / CARBONMONOXIDE-(DICYANO) IRON


Mass: 135.890 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3FeN2O
#7: Chemical ChemComp-H2S / HYDROSULFURIC ACID / HYDROGEN SULFIDE


Mass: 34.081 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H2S
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 319 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsIRON(II) WITH 1 CARBON MONOXIDE AND 2 CYANIDE LIGANDS.

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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 Å3/Da / Density % sol: 38.4 %
Crystal growpH: 6.2 / Details: pH 6.2
Crystal grow
*PLUS
pH: 7.6 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
112 mg/mlprotein1drop
210 mMTris-HCl1drop
32.1 mMDDAO1drop
419-22 %(w/v)PEG80001reservoir
50.1 Msodium chloride1reservoir
60.1 MMES1reservoir

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM02 / Wavelength: 0.98
DetectorDetector: CCD / Date: Oct 1, 1996 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.15→20 Å / Num. obs: 36050 / % possible obs: 93 % / Observed criterion σ(I): 0 / Redundancy: 5.6 % / Biso Wilson estimate: 23.2 Å2 / Rsym value: 0.083
Reflection shellResolution: 2.15→2.18 Å / Rsym value: 0.202 / % possible all: 48.8
Reflection
*PLUS
Num. measured all: 201153 / Rmerge(I) obs: 0.083
Reflection shell
*PLUS
% possible obs: 48.8 % / Rmerge(I) obs: 0.202

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Processing

Software
NameVersionClassification
XDSdata scaling
CCP4data reduction
AMoREphasing
X-PLOR3.857refinement
XDSdata reduction
CCP4data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2FRV

2frv


Resolution: 2.15→8 Å / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.248 1684 4.9 %RANDOM
Rwork0.194 ---
obs-34362 90.1 %-
Displacement parametersBiso mean: 25.7 Å2
Baniso -1Baniso -2Baniso -3
1-0.881 Å20 Å20 Å2
2--0.956 Å20 Å2
3----1.837 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.21 Å
Luzzati d res low-5 Å
Refinement stepCycle: LAST / Resolution: 2.15→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5861 0 34 319 6214
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.84
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.4
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.65
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.320.1
X-RAY DIFFRACTIONx_mcangle_it3.140.2
X-RAY DIFFRACTIONx_scbond_it20.2
X-RAY DIFFRACTIONx_scangle_it4.630.3
LS refinement shellResolution: 2.15→2.25 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.317 140 5 %
Rwork0.263 2641 -
obs--57.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARA.INPTOPO.INP
Software
*PLUS
Name: X-PLOR / Version: 3.857 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.4
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.65

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