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- PDB-5c2w: Kuenenia stuttgartiensis Hydrazine Synthase Pressurized with 20 b... -

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Basic information

Entry
Database: PDB / ID: 5c2w
TitleKuenenia stuttgartiensis Hydrazine Synthase Pressurized with 20 bar Xenon
Components
  • (HYDRAZINE SYNTHASE ...) x 2
  • Hypothetical (Di heme) protein
KeywordsOXIDOREDUCTASE / BETA PROPELLER / HEME C / REDOX ENZYME / ANAMMOX
Function / homology
Function and homology information


hydrazine synthase / anammoxosome / oxidoreductase activity / electron transfer activity / heme binding / metal ion binding
Similarity search - Function
Hydrazine synthase alpha subunit, middle domain / Hydrazine synthase alpha subunit middle domain / YVTN beta-propeller repeat / Cytochrome D1 heme domain / Nitrous oxide reductase, N-terminal / Six-bladed beta-propeller, TolB-like / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / Cytochrome c family profile. ...Hydrazine synthase alpha subunit, middle domain / Hydrazine synthase alpha subunit middle domain / YVTN beta-propeller repeat / Cytochrome D1 heme domain / Nitrous oxide reductase, N-terminal / Six-bladed beta-propeller, TolB-like / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Mainly Beta
Similarity search - Domain/homology
TRIMETHYL GLYCINE / HEME C / XENON / Hydrazine synthase subunit alpha / Hydrazine synthase subunit gamma / Hydrazine synthase subunit beta
Similarity search - Component
Biological speciesCandidatus Kuenenia stuttgartiensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 3.2 Å
AuthorsDietl, A. / Ferousi, C. / Maalcke, W.J. / Menzel, A. / de Vries, S. / Keltjens, J.T. / Jetten, M.S.M. / Kartal, B. / Barends, T.R.M.
CitationJournal: Nature / Year: 2015
Title: The inner workings of the hydrazine synthase multiprotein complex.
Authors: Dietl, A. / Ferousi, C. / Maalcke, W.J. / Menzel, A. / de Vries, S. / Keltjens, J.T. / Jetten, M.S. / Kartal, B. / Barends, T.R.
History
DepositionJun 16, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Oct 14, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 4, 2015Group: Database references
Revision 1.2Dec 2, 2015Group: Database references
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_conn_type
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site.occupancy / _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_alt_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_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_alt_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.pdbx_ptnr1_label_alt_id / _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_type.id
Revision 2.1Jan 10, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HYDRAZINE SYNTHASE ALPHA SUBUNIT
B: HYDRAZINE SYNTHASE BETA SUBUNIT
C: Hypothetical (Di heme) protein
D: HYDRAZINE SYNTHASE ALPHA SUBUNIT
E: HYDRAZINE SYNTHASE BETA SUBUNIT
F: Hypothetical (Di heme) protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)329,45843
Polymers322,4276
Non-polymers7,03237
Water8,953497
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area44890 Å2
ΔGint-506 kcal/mol
Surface area87530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)464.120, 464.120, 145.450
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11C-581-

HOH

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Components

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HYDRAZINE SYNTHASE ... , 2 types, 4 molecules ADBE

#1: Protein HYDRAZINE SYNTHASE ALPHA SUBUNIT


Mass: 87723.945 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Candidatus Kuenenia stuttgartiensis (bacteria)
References: UniProt: Q1Q0T2
#2: Protein HYDRAZINE SYNTHASE BETA SUBUNIT


Mass: 38463.406 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Candidatus Kuenenia stuttgartiensis (bacteria)
References: UniProt: Q1Q0T4

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Protein , 1 types, 2 molecules CF

#3: Protein Hypothetical (Di heme) protein


Mass: 35025.984 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Candidatus Kuenenia stuttgartiensis (bacteria)
References: UniProt: Q1Q0T3

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Non-polymers , 8 types, 534 molecules

#4: Chemical
ChemComp-XE / XENON


Mass: 131.293 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Xe
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Ca
#7: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#8: Chemical
ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#9: Chemical
ChemComp-BET / TRIMETHYL GLYCINE


Mass: 118.154 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C5H12NO2
#10: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 497 / 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: 4.72 Å3/Da / Density % sol: 73.94 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 36% DIOXANE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: May 1, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.2→48.5 Å / Num. obs: 192635 / % possible obs: 100 % / Redundancy: 10.6 % / Rmerge(I) obs: 0.138 / Net I/σ(I): 17.6
Reflection shellResolution: 3.2→3.3 Å / Redundancy: 10.8 % / Rmerge(I) obs: 0.641 / Mean I/σ(I) obs: 4.6 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 5c2v

5c2v


Resolution: 3.2→48.5 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 28.92 / Stereochemistry target values: ML
Details: region around A358-A360 is not well defined in the density
RfactorNum. reflection% reflection
Rfree0.2668 9573 4.97 %
Rwork0.2307 --
obs0.2325 192635 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.2→48.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22448 0 422 497 23367
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00923617
X-RAY DIFFRACTIONf_angle_d1.30932254
X-RAY DIFFRACTIONf_dihedral_angle_d12.7548453
X-RAY DIFFRACTIONf_chiral_restr0.0413297
X-RAY DIFFRACTIONf_plane_restr0.0044189
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.23640.36843150.30426074X-RAY DIFFRACTION100
3.2364-3.27440.36572930.30766161X-RAY DIFFRACTION100
3.2744-3.31430.38193390.30126091X-RAY DIFFRACTION100
3.3143-3.35630.36093410.29426043X-RAY DIFFRACTION100
3.3563-3.40040.32512530.28196192X-RAY DIFFRACTION100
3.4004-3.4470.31683420.28576104X-RAY DIFFRACTION100
3.447-3.49620.32913150.28516032X-RAY DIFFRACTION100
3.4962-3.54840.31663190.27896117X-RAY DIFFRACTION100
3.5484-3.60380.313440.27616070X-RAY DIFFRACTION100
3.6038-3.66290.31763000.27616152X-RAY DIFFRACTION100
3.6629-3.7260.34023140.28076127X-RAY DIFFRACTION100
3.726-3.79380.29943330.26686078X-RAY DIFFRACTION100
3.7938-3.86670.32993150.26916066X-RAY DIFFRACTION100
3.8667-3.94560.29553260.25136097X-RAY DIFFRACTION100
3.9456-4.03140.30162940.24966165X-RAY DIFFRACTION100
4.0314-4.12510.28283240.24366087X-RAY DIFFRACTION100
4.1251-4.22820.28673230.23076091X-RAY DIFFRACTION100
4.2282-4.34240.22383510.2196048X-RAY DIFFRACTION100
4.3424-4.47010.28413050.22046151X-RAY DIFFRACTION100
4.4701-4.61430.25243350.2176080X-RAY DIFFRACTION100
4.6143-4.77910.25073060.22256089X-RAY DIFFRACTION100
4.7791-4.97030.22693330.20496121X-RAY DIFFRACTION100
4.9703-5.19620.2353220.20996092X-RAY DIFFRACTION100
5.1962-5.46980.23142980.20386138X-RAY DIFFRACTION100
5.4698-5.8120.25293390.226096X-RAY DIFFRACTION100
5.812-6.25990.26633120.21656080X-RAY DIFFRACTION100
6.2599-6.88830.24613170.21136112X-RAY DIFFRACTION100
6.8883-7.88130.24323210.20386111X-RAY DIFFRACTION100
7.8813-9.91570.18983230.17366103X-RAY DIFFRACTION100
9.9157-48.52140.16833210.15976094X-RAY DIFFRACTION99

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