PDB-9erc: Hydrogenase-2 Ni-Li state

ID or keywords:

Entry

Database: PDB / ID: 9erc

Title

Hydrogenase-2 Ni-Li state

Components

(Hydrogenase-2 ...) x 2

Keywords

OXIDOREDUCTASE / Hydrogenase / hydrogen

Function / homology

Function and homology information

hydrogenase (acceptor) / ferredoxin hydrogenase complex / [Ni-Fe] hydrogenase complex / hydrogenase (acceptor) activity / ferredoxin hydrogenase activity / anaerobic respiration / 3 iron, 4 sulfur cluster binding / nickel cation binding / iron-sulfur cluster binding / 4 iron, 4 sulfur cluster binding ...
Similarity search - Function

Biological species

Escherichia coli (E. coli)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.308 Å

Authors

Wong, K.L. / Carr, S.B. / Ash, P.A. / Vincent, K.A.

Funding support

United Kingdom, 2items

Organization	Grant number	Country
Biotechnology and Biological Sciences Research Council (BBSRC)	BB/R018413/1	United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)	BB/X002624/1	United Kingdom

Citation

Journal: To Be Published
Title: Glutamate flick enables proton tunnelling during fast redox biocatalysis
Authors: Carr, S.B. / Li, W. / Wong, K.L. / Evans, R.M. / Kendall-Price, S.E.T. / Ash, P.A. / Vincent, K.A.

History

Deposition	Mar 22, 2024	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Apr 2, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9erc.cif.gz	381 KB	Display	PDBx/mmCIF format
PDB format	pdb9erc.ent.gz	289.9 KB	Display	PDB format
PDBx/mmJSON format	9erc.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	9erc_validation.pdf.gz	2.2 MB	Display	wwPDB validaton report
Full document	9erc_full_validation.pdf.gz	2.2 MB	Display
Data in XML	9erc_validation.xml.gz	80.7 KB	Display
Data in CIF	9erc_validation.cif.gz	113 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/er/9erc ftp://data.pdbj.org/pub/pdb/validation_reports/er/9erc	HTTPS FTP

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Related structure data

Related structure data	9eqiC 9eqlC 9er5C 9er6C 9er7C 9er9C 9eraC 9erbC 9erpC 9errC 9ersC C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#111 - Mar 2009 Hydrogenase similarity (19) #144 - Dec 2011 Complex I similarity (3) #220 - Apr 2018 Dehalogenases similarity (2) #154 - Oct 2012 Citric Acid Cycle similarity (1) #241 - Jan 2020 Twenty Years of Molecules similarity (1)

Deposited unit

S: Hydrogenase-2 small chain

L: Hydrogenase-2 large chain

T: Hydrogenase-2 small chain

M: Hydrogenase-2 large chain

hetero molecules

194 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	99.877, 99.974, 168.071
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	S
2	1	T
3	2	L
4	2	M

NCS domain segments:

Beg auth comp-ID: GLN / Beg label comp-ID: GLN / End auth comp-ID: VAL / End label comp-ID: VAL

Dom-ID	Component-ID	Ens-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	1	S	A	10 - 275	9 - 274
2	1	1	T	C	10 - 275	9 - 274
3	2	2	L	B	3 - 551	3 - 551
4	2	2	M	D	3 - 551	3 - 551

NCS ensembles :

ID	Details
1	Local NCS retraints between domains: 1 2
2	Local NCS retraints between domains: 3 4

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Hydrogenase-2 ... , 2 types, 4 molecules STLM

#1: Protein	Hydrogenase-2 small chain / HYD2 / Membrane-bound hydrogenase 2 small subunit / NiFe hydrogenase Mass: 32371.498 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: hybO, yghV, b2997, JW2965 / Plasmid: pOC / Production host: Escherichia coli (E. coli) / Strain (production host): HJ001-hyp / References: UniProt: P69741, hydrogenase (acceptor)
#2: Protein	Hydrogenase-2 large chain / HYD2 / Membrane-bound hydrogenase 2 large subunit / NiFe hydrogenase Mass: 62557.906 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: hybC, b2994, JW2962 / Production host: Escherichia coli (E. coli) / Strain (production host): HJ001-hyp / References: UniProt: P0ACE0, hydrogenase (acceptor)

#1: Protein

Hydrogenase-2 small chain / HYD2 / Membrane-bound hydrogenase 2 small subunit / NiFe hydrogenase

Mass: 32371.498 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Escherichia coli (E. coli) / Gene: hybO, yghV, b2997, JW2965 / Plasmid: pOC / Production host:

Escherichia coli (E. coli) / Strain (production host): HJ001-hyp / References: UniProt: P69741, hydrogenase (acceptor)

#2: Protein

Hydrogenase-2 large chain / HYD2 / Membrane-bound hydrogenase 2 large subunit / NiFe hydrogenase

Mass: 62557.906 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Escherichia coli (E. coli) / Gene: hybC, b2994, JW2962 / Production host:

Escherichia coli (E. coli) / Strain (production host): HJ001-hyp / References: UniProt: P0ACE0, hydrogenase (acceptor)

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Non-polymers , 7 types, 1377 molecules

#3: Chemical	ChemComp-SF4 / IRON/SULFUR CLUSTER Mass: 351.640 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe₄S₄
#4: Chemical	ChemComp-F3S / FE3-S4 CLUSTER Mass: 295.795 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe₃S₄
#5: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C₃H₈O₃
#6: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#7: Chemical	ChemComp-FCO / CARBONMONOXIDE-(DICYANO) IRON Mass: 135.890 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃FeN₂O / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical	ChemComp-NI / NICKEL (II) ION Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni / Feature type: SUBJECT OF INVESTIGATION
#9: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1344 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	Y
Has protein modification	N

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.21 Å³/Da / Density % sol: 44.34 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 100 mM BisTris 200 mM MgCl2 20% PEG 3350 Temp details: Ambient temperature inside an anaerobic glovebox

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.6199 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 23, 2023
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.6199 Å / Relative weight: 1
Reflection	Resolution: 1.308→100 Å / Num. obs: 402048 / % possible obs: 100 % / Redundancy: 13.9 % / CC_1/2: 0.998 / R_merge(I) obs: 0.215 / R_pim(I) all: 0.06 / Net I/σ(I): 5.8
Reflection shell	Resolution: 1.31→1.33 Å / Redundancy: 14 % / R_merge(I) obs: 3.78 / Mean I/σ(I) obs: 0.3 / Num. unique obs: 19627 / CC_1/2: 0.313 / R_pim(I) all: 1.04 / % possible all: 99.8

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0405	refinement
DIALS		data reduction
Aimless		data scaling
REFMAC		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.308→86.07 Å / Cor.coef. F_o:F_c: 0.978 / Cor.coef. F_o:F_c free: 0.971 / SU B: 1.797 / SU ML: 0.062 / Cross valid method: FREE R-VALUE / ESU R: 0.048 / ESU R Free: 0.049
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.193	1979	0.505 %
R_work	0.1739	390097	-
all	0.174	-	-
obs	-	392076	97.452 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 16.634 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.019 Å²	0 Å²	-0 Å²
2-	-	0.643 Å²	0 Å²
3-	-	-	-0.663 Å²

Refinement step

Cycle: LAST / Resolution: 1.308→86.07 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	12639	0	160	1344	14143

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.012	13339
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	12319
X-RAY DIFFRACTION	r_angle_refined_deg	1.546	1.652	18223
X-RAY DIFFRACTION	r_angle_other_deg	0.531	1.573	28460
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.249	5	1686
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	6.76	5	58
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.399	10	2092
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	16.746	10	585
X-RAY DIFFRACTION	r_chiral_restr	0.081	0.2	1999
X-RAY DIFFRACTION	r_chiral_restr_other	0.007	0.2	1
X-RAY DIFFRACTION	r_gen_planes_refined	0.009	0.02	15568
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	2950
X-RAY DIFFRACTION	r_nbd_refined	0.223	0.2	2887
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.184	0.2	12474
X-RAY DIFFRACTION	r_nbtor_refined	0.181	0.2	6652
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.078	0.2	6916
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.16	0.2	1126
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.146	0.2	3
X-RAY DIFFRACTION	r_metal_ion_refined	0.086	0.2	30
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.179	0.2	14
X-RAY DIFFRACTION	r_nbd_other	0.187	0.2	39
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.202	0.2	22
X-RAY DIFFRACTION	r_mcbond_it	1.275	1.624	6651
X-RAY DIFFRACTION	r_mcbond_other	1.274	1.624	6650
X-RAY DIFFRACTION	r_mcangle_it	1.751	2.915	8341
X-RAY DIFFRACTION	r_mcangle_other	1.751	2.915	8342
X-RAY DIFFRACTION	r_scbond_it	2.58	1.877	6688
X-RAY DIFFRACTION	r_scbond_other	2.58	1.877	6689
X-RAY DIFFRACTION	r_scangle_it	3.988	3.316	9813
X-RAY DIFFRACTION	r_scangle_other	3.988	3.316	9814
X-RAY DIFFRACTION	r_lrange_it	5.072	17.161	15786
X-RAY DIFFRACTION	r_lrange_other	5.072	17.113	15782
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.06	0.05	8684
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.053	0.05	19343

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)	Weight position
1	1	S	X-RAY DIFFRACTION	Local ncs	0.06022	0.0501
1	2	S	X-RAY DIFFRACTION	Local ncs	0.06022	0.0501
2	3	S	X-RAY DIFFRACTION	Local ncs	0.05314	0.0501
2	4	S	X-RAY DIFFRACTION	Local ncs	0.05314	0.0501

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
1.308-1.342	0.351	120	0.401	21351	0.401	29514	0.886	0.868	72.7485	0.398
1.342-1.379	0.383	136	0.386	26592	0.386	28804	0.89	0.878	92.7927	0.384
1.379-1.419	0.367	161	0.372	27762	0.372	28048	0.895	0.89	99.5543	0.371
1.419-1.463	0.296	126	0.351	27098	0.351	27229	0.921	0.902	99.9816	0.352
1.463-1.511	0.325	119	0.319	26326	0.319	26446	0.925	0.919	99.9962	0.322
1.511-1.564	0.269	149	0.283	25407	0.283	25557	0.949	0.936	99.9961	0.285
1.564-1.623	0.251	115	0.251	24496	0.251	24611	0.954	0.953	100	0.248
1.623-1.689	0.219	125	0.216	23645	0.216	23770	0.965	0.966	100	0.207
1.689-1.764	0.218	102	0.196	22685	0.196	22787	0.971	0.974	100	0.18
1.764-1.85	0.193	131	0.172	21730	0.172	21861	0.975	0.98	100	0.153
1.85-1.95	0.198	105	0.161	20638	0.161	20743	0.975	0.983	100	0.143
1.95-2.068	0.181	94	0.154	19598	0.155	19692	0.983	0.986	100	0.138
2.068-2.211	0.178	86	0.143	18426	0.143	18512	0.982	0.989	100	0.127
2.211-2.388	0.173	72	0.134	17213	0.134	17285	0.983	0.99	100	0.117
2.388-2.616	0.133	80	0.123	15841	0.123	15921	0.988	0.991	100	0.105
2.616-2.924	0.179	78	0.122	14353	0.123	14431	0.981	0.991	100	0.104
2.924-3.376	0.137	64	0.122	12743	0.122	12807	0.989	0.991	100	0.106
3.376-4.133	0.135	53	0.113	10823	0.113	10876	0.989	0.992	100	0.102
4.133-5.838	0.158	49	0.13	8485	0.13	8534	0.99	0.993	100	0.122
5.838-86.07	0.145	14	0.184	4886	0.184	4900	0.988	0.976	100	0.179

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