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- PDB-3lx4: Stepwise [FeFe]-hydrogenase H-cluster assembly revealed in the st... -

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Basic information

Entry
Database: PDB / ID: 3lx4
TitleStepwise [FeFe]-hydrogenase H-cluster assembly revealed in the structure of HydA(deltaEFG)
ComponentsFe-hydrogenase
KeywordsOXIDOREDUCTASE / Hydrogenase / HydA / Hydrogen / H-cluster / [4Fe-4S] cluster / Iron-sulfur cluster / Insertion / Biosynthesis / Maturation / Intermediate / Evolution
Function / homology
Function and homology information


1.18.99.1 / 4 iron, 4 sulfur cluster binding / oxidoreductase activity / metal ion binding
Similarity search - Function
Rossmann fold - #1780 / Fe-only Hydrogenase (Larger Subunit); Chain L, domain 3 / Fe-only Hydrogenase (Larger Subunit); Chain L, domain 3 / 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 / Rossmann fold ...Rossmann fold - #1780 / Fe-only Hydrogenase (Larger Subunit); Chain L, domain 3 / Fe-only Hydrogenase (Larger Subunit); Chain L, domain 3 / 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 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / IRON/SULFUR CLUSTER / Fe-hydrogenase
Similarity search - Component
Biological speciesChlamydomonas reinhardtii (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.97 Å
AuthorsMulder, D.W. / Boyd, E.S. / Sarma, R. / Lange, R.K. / Endrizzi, J.A. / Broderick, J.B. / Peters, J.W.
CitationJournal: Nature / Year: 2010
Title: Stepwise [FeFe]-hydrogenase H-cluster assembly revealed in the structure of HydA(DeltaEFG).
Authors: Mulder, D.W. / Boyd, E.S. / Sarma, R. / Lange, R.K. / Endrizzi, J.A. / Broderick, J.B. / Peters, J.W.
History
DepositionFeb 24, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 28, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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_ncs_dom_lim / 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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details / _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
A: Fe-hydrogenase
B: Fe-hydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,6248
Polymers98,7322
Non-polymers8926
Water13,962775
1
A: Fe-hydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,8124
Polymers49,3661
Non-polymers4463
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Fe-hydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,8124
Polymers49,3661
Non-polymers4463
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)70.895, 70.895, 155.429
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number145
Space group name H-MP32
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Ens-ID: 1 / Refine code: 4

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LEULEUALAALAAA25 - 11525 - 115
21LEULEUALAALABB25 - 11525 - 115
12GLUGLUASPASPAA121 - 200121 - 200
22GLUGLUASPASPBB121 - 200121 - 200
13LEULEUALAALAAA205 - 311205 - 311
23LEULEUALAALABB205 - 311205 - 311
14GLYGLYVALVALAA323 - 450323 - 450
24GLYGLYVALVALBB323 - 450323 - 450

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Components

#1: Protein Fe-hydrogenase / Iron hydrogenase / Iron-hydrogenase HydA1


Mass: 49366.090 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlamydomonas reinhardtii (plant) / Gene: CHLREDRAFT_183963, hyd1, hydA, hydA1 / Plasmid: pET Duet / Production host: Escherichia coli (E. coli) / References: UniProt: Q9FYU1, 1.18.99.1
#2: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S4
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 775 / 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: 2.28 Å3/Da / Density % sol: 46.15 %
Crystal growTemperature: 298 K / Method: capillary batch diffusion / pH: 6.5
Details: 25.5% PEG 8000, 0.085 M sodium cacodylate, 0.17 M sodium acetate trihydrate, 1 mM dithionite, pH 6.5, capillary batch diffusion, temperature 298.0K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.95369 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 10, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95369 Å / Relative weight: 1
ReflectionResolution: 1.97→50 Å / Num. obs: 60782 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.4 %
Reflection shellResolution: 1.97→2.04 Å / Redundancy: 4.2 % / Mean I/σ(I) obs: 2.4 / Num. unique all: 10553 / Rsym value: 0.409 / % possible all: 97.2

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3.5 Å29.25 Å
Translation3.5 Å29.25 Å

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Processing

Software
NameVersionClassificationNB
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1FEH

1feh


Resolution: 1.97→20 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.93 / WRfactor Rfree: 0.215 / WRfactor Rwork: 0.173 / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.859 / SU B: 3.432 / SU ML: 0.1 / SU R Cruickshank DPI: 0.166 / SU Rfree: 0.152 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.166 / ESU R Free: 0.152 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.216 3074 5.1 %RANDOM
Rwork0.17 ---
obs0.173 57708 97.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 96.43 Å2 / Biso mean: 26.922 Å2 / Biso min: 3.69 Å2
Baniso -1Baniso -2Baniso -3
1--1.16 Å2-0.58 Å20 Å2
2---1.16 Å20 Å2
3---1.73 Å2
Refinement stepCycle: LAST / Resolution: 1.97→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6166 0 26 775 6967
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0226346
X-RAY DIFFRACTIONr_angle_refined_deg0.9241.9898606
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7545822
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.18224.048252
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.038151094
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.5821540
X-RAY DIFFRACTIONr_chiral_restr0.0650.2970
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.024734
X-RAY DIFFRACTIONr_nbd_refined0.2040.32980
X-RAY DIFFRACTIONr_nbtor_refined0.3080.54324
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1960.5968
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1280.346
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2330.557
X-RAY DIFFRACTIONr_mcbond_it4.154154168
X-RAY DIFFRACTIONr_mcangle_it5.056206488
X-RAY DIFFRACTIONr_scbond_it7.288252432
X-RAY DIFFRACTIONr_scangle_it9.824402086
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Number: 3088 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDTypeRms dev position (Å)Weight position
AMEDIUM POSITIONAL0.090.5
BMEDIUM THERMAL0.392
LS refinement shellResolution: 1.97→2.016 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.291 204 -
Rwork0.22 4125 -
all-4329 -
obs--95.67 %

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