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- PDB-6hif: Kuenenia stuttgartiensis hydrazine dehydrogenase complex -

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Basic information

Entry
Database: PDB / ID: 6hif
TitleKuenenia stuttgartiensis hydrazine dehydrogenase complex
Components
  • Hydrazine dehydrogenase
  • hdh assembly factor Kustc1130
KeywordsOXIDOREDUCTASE / anammox / hydrazine / dehydrogenase / P460 / redox
Function / homology
Function and homology information


hydrazine dehydrogenase / hydroxylamine oxidoreductase activity / anammoxosome / membrane => GO:0016020 / metal ion binding
Similarity search - Function
Seven times multi-haem cytochrome CxxCH / Carboxypeptidase-like, regulatory domain superfamily / Multiheme cytochrome c family profile. / Multiheme cytochrome superfamily
Similarity search - Domain/homology
HEME C / : / Uncharacterized protein / Hydrazine dehydrogenase / Assembly factor of hydrazine dehydrogenase
Similarity search - Component
Biological speciesKuenenia stuttgartiensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsAkram, M. / Dietl, A. / Mersdorf, U. / Prinz, S. / Maalcke, W. / Keltjens, J. / Ferousi, C. / de Almeida, N.M. / Reimann, J. / Kartal, B. ...Akram, M. / Dietl, A. / Mersdorf, U. / Prinz, S. / Maalcke, W. / Keltjens, J. / Ferousi, C. / de Almeida, N.M. / Reimann, J. / Kartal, B. / Jetten, M.S.M. / Parey, K. / Barends, T.R.M.
CitationJournal: Sci Adv / Year: 2019
Title: A 192-heme electron transfer network in the hydrazine dehydrogenase complex.
Authors: M Akram / A Dietl / U Mersdorf / S Prinz / W Maalcke / J Keltjens / C Ferousi / N M de Almeida / J Reimann / B Kartal / M S M Jetten / K Parey / T R M Barends /
Abstract: Anaerobic ammonium oxidation (anammox) is a major process in the biogeochemical nitrogen cycle in which nitrite and ammonium are converted to dinitrogen gas and water through the highly reactive ...Anaerobic ammonium oxidation (anammox) is a major process in the biogeochemical nitrogen cycle in which nitrite and ammonium are converted to dinitrogen gas and water through the highly reactive intermediate hydrazine. So far, it is unknown how anammox organisms convert the toxic hydrazine into nitrogen and harvest the extremely low potential electrons (-750 mV) released in this process. We report the crystal structure and cryo electron microscopy structures of the responsible enzyme, hydrazine dehydrogenase, which is a 1.7 MDa multiprotein complex containing an extended electron transfer network of 192 heme groups spanning the entire complex. This unique molecular arrangement suggests a way in which the protein stores and releases the electrons obtained from hydrazine conversion, the final step in the globally important anammox process.
History
DepositionAug 29, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 17, 2019Provider: repository / Type: Initial release
Revision 1.1May 1, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jan 17, 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_database_related / 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_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
G: Hydrazine dehydrogenase
A: Hydrazine dehydrogenase
B: Hydrazine dehydrogenase
C: Hydrazine dehydrogenase
D: Hydrazine dehydrogenase
E: Hydrazine dehydrogenase
F: Hydrazine dehydrogenase
H: Hydrazine dehydrogenase
I: Hydrazine dehydrogenase
J: Hydrazine dehydrogenase
K: Hydrazine dehydrogenase
L: Hydrazine dehydrogenase
M: Hydrazine dehydrogenase
N: Hydrazine dehydrogenase
O: Hydrazine dehydrogenase
P: Hydrazine dehydrogenase
Q: Hydrazine dehydrogenase
R: Hydrazine dehydrogenase
S: Hydrazine dehydrogenase
T: Hydrazine dehydrogenase
U: Hydrazine dehydrogenase
V: Hydrazine dehydrogenase
W: Hydrazine dehydrogenase
X: Hydrazine dehydrogenase
Y: hdh assembly factor Kustc1130
Z: hdh assembly factor Kustc1130
a: hdh assembly factor Kustc1130
b: hdh assembly factor Kustc1130
c: hdh assembly factor Kustc1130
d: hdh assembly factor Kustc1130
e: hdh assembly factor Kustc1130
f: hdh assembly factor Kustc1130
g: hdh assembly factor Kustc1130
h: hdh assembly factor Kustc1130
i: hdh assembly factor Kustc1130
j: hdh assembly factor Kustc1130
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,846,125322
Polymers1,718,64236
Non-polymers127,483286
Water16,844935
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)211.860, 211.860, 398.570
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11G
21A
31B
41C
51E
61F
71H
81J
91K
101L
111M
121N
131O
141P
151Q
161R
171S
181T
191U
201V
211W
221X
12Y
22Z
32a
42b
52c
62d
72e
82f
92g
102h
112i

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111G33 - 607
2111A33 - 607
3111B33 - 607
4111C33 - 607
5111E33 - 607
6111F33 - 607
7111H33 - 607
8111J33 - 607
9111K33 - 607
10111L33 - 607
11111M33 - 607
12111N33 - 607
13111O33 - 607
14111P33 - 607
15111Q33 - 607
16111R33 - 607
17111S33 - 607
18111T33 - 607
19111U33 - 607
20111V33 - 607
21111W33 - 607
22111X33 - 607
1121Y1 - 111
2121Z1 - 111
3121a1 - 111
4121b1 - 111
5121c1 - 111
6121d1 - 111
7121e1 - 111
8121f1 - 111
9121g1 - 111
10121h1 - 111
11121i1 - 111

NCS ensembles :
ID
1
2

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.550655, -0.833165, 0.051146), (-0.242777, -0.218478, -0.94516), (0.798648, 0.50804, -0.322579)-61.61349, -133.87224, -20.92837
3given(-0.497412, -0.857031, -0.134457), (0.867513, -0.491673, -0.075356), (-0.001527, -0.154126, 0.98805)-108.20892, -63.21834, -10.52693
4given(0.165028, -0.464418, -0.870105), (-0.469433, -0.812852, 0.344825), (-0.867409, 0.35155, -0.352156)-105.85678, -101.81544, -86.71943
5given(0.971995, 0.188483, 0.140358), (0.19535, -0.980045, -0.036746), (0.130632, 0.063136, -0.989419)20.67188, -110.48939, -108.86688
6given(0.399784, -0.396245, 0.826537), (0.914933, 0.227027, -0.333702), (-0.055419, 0.889634, 0.453299)6.96863, -32.32632, 18.09803
7given(0.433468, 0.43701, -0.788117), (0.883439, -0.033442, 0.467352), (0.177881, -0.898835, -0.400567)-39.6539, -3.31764, -128.53102
8given(-0.460778, 0.423857, -0.779762), (0.342057, -0.725903, -0.59671), (-0.818951, -0.541674, 0.189497)-67.17307, -122.79621, -106.9444
9given(0.596776, 0.294502, -0.74641), (-0.799973, 0.145956, -0.582013), (-0.062461, 0.944439, 0.322696)-37.80552, -108.72627, 12.81989
10given(-0.041819, -0.55505, -0.830765), (0.524746, 0.695378, -0.49101), (0.850231, -0.456474, 0.26218)-113.5695, -27.42957, -42.48684
11given(0.386089, 0.921409, -0.044067), (-0.308061, 0.173817, 0.935354), (0.869502, -0.347554, 0.350958)33.23485, -2.52161, -29.92702
12given(-0.653985, 0.748349, 0.110807), (0.756508, 0.647053, 0.094966), (-0.00063, 0.145933, -0.989294)-2.868, 12.1323, -108.24948
13given(0.048959, 0.490058, 0.870314), (-0.603031, 0.709125, -0.365372), (-0.796214, -0.506938, 0.330238)49.81445, -56.80348, -96.59148
14given(-0.486208, 0.208527, -0.848598), (-0.47566, 0.751479, 0.457194), (0.733041, 0.625936, -0.266188)-86.80689, -3.80567, -12.70806
15given(-0.996209, -0.076006, 0.042315), (-0.072252, 0.452024, -0.889075), (0.048448, -0.888761, -0.455803)-68.9128, -85.85243, -135.3855
16given(-0.500199, 0.865846, -0.010557), (-0.855868, -0.496213, -0.145819), (-0.131495, -0.063903, 0.989255)-0.14199, -124.62775, -9.36486
17given(-0.552353, -0.263672, 0.790812), (-0.258274, -0.847849, -0.463084), (0.792591, -0.460032, 0.400212)-19.32534, -142.03154, -36.55918
18given(-0.97698, -0.120142, -0.176285), (-0.110478, -0.421967, 0.899855), (-0.182496, 0.898615, 0.39898)-81.09895, -33.02619, 10.51546
19given(-0.32419, -0.945991, 0.001626), (-0.945991, 0.324191, 0.000645), (-0.001137, -0.001329, -0.999998)-97.38661, -69.46747, -117.30188
20given(0.557551, -0.23419, 0.796424), (-0.828088, -0.22435, 0.513748), (0.058363, -0.94595, -0.319017)17.36384, -70.0182, -130.76134
21given(-0.167605, 0.548321, 0.8193), (0.545692, -0.640533, 0.540312), (0.821053, 0.537645, -0.191857)40.48111, -46.80859, -10.1693
22given(-0.482383, -0.468494, 0.740148), (0.215161, 0.755699, 0.618566), (-0.849124, 0.457638, -0.263735)-34.67286, 29.09695, -75.18567

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Components

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Protein , 2 types, 36 molecules GABCDEFHIJKLMNOPQRSTUVWXYZabcd...

#1: Protein ...
Hydrazine dehydrogenase / HDH / Octaheme c-type cytochrome kustc0694


Mass: 65673.766 Da / Num. of mol.: 24 / Source method: isolated from a natural source / Source: (natural) Kuenenia stuttgartiensis (bacteria) / References: UniProt: Q1PW30, hydrazine dehydrogenase
#2: Protein
hdh assembly factor Kustc1130


Mass: 11872.622 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Kuenenia stuttgartiensis (bacteria) / References: UniProt: Q1PXB2, UniProt: A0A2C9CI58*PLUS

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Non-polymers , 5 types, 1221 molecules

#3: Chemical...
ChemComp-HEC / HEME C / Heme C


Mass: 618.503 Da / Num. of mol.: 192 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#4: Chemical...
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 72 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 935 / 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: 3 Å3/Da / Density % sol: 59.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 1+1 ul hanging drops against a reservoir solution containing 8-9% (w/v) polyethylene glycol 4000, 0.25 M (NH4)2SO4.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.95376 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 10, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95376 Å / Relative weight: 1
ReflectionResolution: 2.8→185 Å / Num. obs: 452098 / % possible obs: 96.6 % / Redundancy: 2 % / CC1/2: 0.989 / Rmerge(I) obs: 0.111 / Rrim(I) all: 0.147 / Net I/σ(I): 6.67
Reflection shellResolution: 2.8→2.9 Å / Rmerge(I) obs: 0.745 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 49339 / CC1/2: 0.457 / Rrim(I) all: 0.994 / % possible all: 98.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0222refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4N4J

4n4j


Resolution: 2.8→93.71 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.915 / SU B: 19.245 / SU ML: 0.338 / Cross valid method: THROUGHOUT / ESU R Free: 0.352 / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.23838 24032 5 %RANDOM
Rwork0.22108 ---
obs0.222 452098 96.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 63.322 Å2
Baniso -1Baniso -2Baniso -3
1--0.46 Å2-0.23 Å2-0 Å2
2---0.46 Å2-0 Å2
3---1.5 Å2
Refinement stepCycle: 1 / Resolution: 2.8→93.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms109079 0 8728 935 118742
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.012123148
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.9471.771168372
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.284513738
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.19322.296121
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.8631518073
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.08315649
X-RAY DIFFRACTIONr_chiral_restr0.0670.214080
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.03196758
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.1076.38355057
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.5189.56968760
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.2186.25668091
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined6.85982.809194530
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: tight thermal / Weight position: 0.5

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11G455920.79
11A45595.74
11B45596.98
11C45597.45
11E455912.38
11F455917.01
11H455921.03
11J455918.05
11K455916.83
11L455915.84
11M45597.66
11N45595.94
11O455910.33
11P455910.52
11Q45597.02
11R45599.71
11S455920.92
11T455916.17
11U455920.25
11V455919.29
11W455920.37
11X455923.7
22Y64033.62
22Z64013.87
22a6406.1
22b6406.31
22c6409.99
22d64014.06
22e6408.82
22f64012.15
22g6405.69
22h64015.18
22i64024.58
LS refinement shellResolution: 2.8→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.509 4 -
Rwork0.365 35991 -
obs--98.82 %

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