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- PDB-6de6: 2.1 A resolution structure of histamine dehydrogenase from Rhizob... -

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Basic information

Entry
Database: PDB / ID: 6de6
Title2.1 A resolution structure of histamine dehydrogenase from Rhizobium sp. 4-9
ComponentsHistamine dehydrogenase
KeywordsOXIDOREDUCTASE / histamine dehydrogenase / FMN binding / 4Fe-4S cluster
Function / homology
Function and homology information


FMN binding / oxidoreductase activity
Similarity search - Function
Trimethylamine dehydrogenase/Dimethylamine dehydrogenase, FMN-binding domain / NADH:flavin oxidoreductase/NADH oxidase, N-terminal / NADH:flavin oxidoreductase / NADH oxidase family / FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase / FAD/NAD(P)-binding domain superfamily / Aldolase-type TIM barrel
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / FLAVIN MONONUCLEOTIDE / PHOSPHATE ION / IRON/SULFUR CLUSTER / Histamine dehydrogenase
Similarity search - Component
Biological speciesRhizobium sp. 4-9 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsGoyal, P. / Lovell, S. / Richter, M.
CitationJournal: Arch.Biochem.Biophys. / Year: 2023
Title: Structure of Rhizobium sp. 4-9 histamine dehydrogenase and analysis of the electron transfer pathway to an abiological electron acceptor.
Authors: Goyal, P. / Deay 3rd, D. / Seibold, S. / Candido, A.C.L. / Lovell, S. / Battaile, K.P. / Wilson, G.S. / Richter, M.L. / Petillo, P.A.
History
DepositionMay 11, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 15, 2019Provider: repository / Type: Initial release
Revision 1.1May 17, 2023Group: Database references / Derived calculations / Refinement description
Category: citation / citation_author ...citation / citation_author / database_2 / struct_conn / struct_ncs_dom_lim
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_seq_id / _struct_conn.ptnr1_label_asym_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_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
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Histamine dehydrogenase
B: Histamine dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)156,7669
Polymers154,2012
Non-polymers2,5657
Water9,980554
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12810 Å2
ΔGint-98 kcal/mol
Surface area43070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.223, 105.314, 140.038
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 4 through 130 or (resid 131...
21(chain B and ((resid 4 and (name N or name...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASNASNTHRTHR(chain A and (resid 4 through 130 or (resid 131...AA4 - 1307 - 133
12PHEPHEPHEPHE(chain A and (resid 4 through 130 or (resid 131...AA131134
13ASNASNPROPRO(chain A and (resid 4 through 130 or (resid 131...AA4 - 6927 - 695
14ASNASNPROPRO(chain A and (resid 4 through 130 or (resid 131...AA4 - 6927 - 695
15ASNASNPROPRO(chain A and (resid 4 through 130 or (resid 131...AA4 - 6927 - 695
16ASNASNPROPRO(chain A and (resid 4 through 130 or (resid 131...AA4 - 6927 - 695
21ASNASNASNASN(chain B and ((resid 4 and (name N or name...BB47
22ARGARGPROPRO(chain B and ((resid 4 and (name N or name...BB2 - 6925 - 695
23ARGARGPROPRO(chain B and ((resid 4 and (name N or name...BB2 - 6925 - 695
24ARGARGPROPRO(chain B and ((resid 4 and (name N or name...BB2 - 6925 - 695
25ARGARGPROPRO(chain B and ((resid 4 and (name N or name...BB2 - 6925 - 695
26ARGARGPROPRO(chain B and ((resid 4 and (name N or name...BB2 - 6925 - 695

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Histamine dehydrogenase


Mass: 77100.250 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhizobium sp. 4-9 (bacteria) / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q60I59

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Non-polymers , 5 types, 561 molecules

#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P
#4: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S4
#5: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 554 / 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: 2.47 Å3/Da / Density % sol: 50.16 % / Mosaicity: 0.18 °
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.1M Na HEPES, 18% w/v PEG 12000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 4, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→48.43 Å / Num. obs: 89613 / % possible obs: 100 % / Redundancy: 6.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.106 / Rpim(I) all: 0.045 / Rrim(I) all: 0.115 / Net I/σ(I): 12.7 / Num. measured all: 586744 / Scaling rejects: 82
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 6.5 % / Rmerge(I) obs: 1.222 / Num. unique obs: 4554 / CC1/2: 0.64 / Rpim(I) all: 0.519 / Rrim(I) all: 1.329 / % possible all: 99.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation5.09 Å48.43 Å
Translation5.09 Å48.43 Å

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimless0.6.2data scaling
PHASER2.8.2phasing
PHENIXrefinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3k30

3k30


Resolution: 2.1→48.427 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.01 / Phase error: 20.44
RfactorNum. reflection% reflection
Rfree0.2022 4463 4.99 %
Rwork0.164 --
obs0.166 89514 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 90.52 Å2 / Biso mean: 37.0718 Å2 / Biso min: 20.17 Å2
Refinement stepCycle: final / Resolution: 2.1→48.427 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10303 0 137 554 10994
Biso mean--35.05 37.87 -
Num. residues----1341
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A6002X-RAY DIFFRACTION6.227TORSIONAL
12B6002X-RAY DIFFRACTION6.227TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1-2.12390.27691530.232227682921100
2.1239-2.14890.28261500.230128382988100
2.1489-2.17510.2771280.221327872915100
2.1751-2.20260.25471590.211228262985100
2.2026-2.23160.2721720.213827702942100
2.2316-2.26210.28361460.240727862932100
2.2621-2.29450.26261230.194928692992100
2.2945-2.32870.24031480.192527622910100
2.3287-2.36510.23431470.179828112958100
2.3651-2.40390.23991300.177728392969100
2.4039-2.44530.23151610.174427922953100
2.4453-2.48980.24631350.173428152950100
2.4898-2.53770.22131540.164428092963100
2.5377-2.58950.22041530.163728252978100
2.5895-2.64580.18981620.162628062968100
2.6458-2.70730.21981090.161528602969100
2.7073-2.7750.19131310.167128552986100
2.775-2.850.21881430.168728242967100
2.85-2.93390.23251550.170628262981100
2.9339-3.02860.21261580.170228142972100
3.0286-3.13680.20631630.176928302993100
3.1368-3.26240.22961450.188728332978100
3.2624-3.41080.21121740.170728192993100
3.4108-3.59060.2051380.168428512989100
3.5906-3.81540.18421740.148128303004100
3.8154-4.10990.18021670.137728403007100
4.1099-4.52320.14281300.124529113041100
4.5232-5.17710.1381610.119828803041100
5.1771-6.52010.16721470.156229333080100
6.5201-48.44010.21811470.17453042318999

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