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- PDB-1upx: The crystal structure of the Hybrid Cluster Protein from Desulfov... -

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Basic information

Entry
Database: PDB / ID: 1upx
TitleThe crystal structure of the Hybrid Cluster Protein from Desulfovibrio desulfuricans containing molecules in the oxidized and reduced states.
ComponentsHYDROXYLAMINE REDUCTASE
KeywordsOXIDOREDUCTASE / HYBRID CLUSTER / REDUCED IRON-SULFUR / OXIDIZED IRON-SULFUR
Function / homology
Function and homology information


hydroxylamine reductase / hydroxylamine reductase activity / peroxidase activity / response to hydrogen peroxide / 4 iron, 4 sulfur cluster binding / metal ion binding / cytoplasm
Similarity search - Function
Substrate Binding Domain Of Dnak; Chain:A; Domain 2 - #20 / Hydroxylamine reductase / Prismane, alpha-bundle / Rossmann fold - #2030 / Hydroxylamine reductase/Ni-containing CO dehydrogenase / Prismane/CO dehydrogenase family / Prismane-like, alpha/beta-sandwich / Prismane-like superfamily / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 / Up-down Bundle ...Substrate Binding Domain Of Dnak; Chain:A; Domain 2 - #20 / Hydroxylamine reductase / Prismane, alpha-bundle / Rossmann fold - #2030 / Hydroxylamine reductase/Ni-containing CO dehydrogenase / Prismane/CO dehydrogenase family / Prismane-like, alpha/beta-sandwich / Prismane-like superfamily / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 / Up-down Bundle / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
IRON/SULFUR/OXYGEN HYBRID CLUSTER / FE4-S3 CLUSTER / IRON/SULFUR CLUSTER / Hydroxylamine reductase
Similarity search - Component
Biological speciesDESULFOVIBRIO DESULFURICANS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å
AuthorsAragao, D. / Macedo, S. / Mitchell, E.P. / Lindley, P.F.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2003
Title: Structure of the Hybrid Cluster Protein (Hcp) from Desulfovibrio Desulfuricans Atcc 27774 Containing Molecules in the Oxidized and Reduced States
Authors: Macedo, S. / Aragao, D. / Mitchell, E.P. / Lindley, P.F.
History
DepositionOct 14, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 2, 2003Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Atomic model / Version format compliance
Revision 1.2May 8, 2019Group: Advisory / Data collection ...Advisory / Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / pdbx_unobs_or_zero_occ_atoms / struct_biol
Item: _exptl_crystal_grow.method / _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.3Dec 23, 2020Group: Advisory / Derived calculations / Other
Category: database_PDB_caveat / pdbx_database_status ...database_PDB_caveat / pdbx_database_status / pdbx_struct_conn_angle / struct_conn
Item: _pdbx_database_status.status_code_sf / _struct_conn.pdbx_dist_value ..._pdbx_database_status.status_code_sf / _struct_conn.pdbx_dist_value / _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
Revision 1.4Mar 29, 2023Group: Advisory / Database references / Structure summary
Category: audit_author / database_2 / pdbx_unobs_or_zero_occ_atoms
Item: _audit_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Feb 7, 2024Group: 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

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Assembly

Deposited unit
A: HYDROXYLAMINE REDUCTASE
B: HYDROXYLAMINE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,4659
Polymers117,1922
Non-polymers2,2737
Water30,2111677
1
A: HYDROXYLAMINE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,6354
Polymers58,5961
Non-polymers1,0393
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: HYDROXYLAMINE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,8305
Polymers58,5961
Non-polymers1,2344
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)57.300, 61.200, 72.000
Angle α, β, γ (deg.)82.80, 73.70, 87.30
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.9807, -0.1955, -0.0081), (-0.1956, -0.9792, -0.0544), (0.0027, 0.055, -0.9985)
Vector: -43.5791, 45.9457, 30.6063)

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein HYDROXYLAMINE REDUCTASE / PRISMANE PROTEIN / HYBRID-CLUSTER PROTEIN / HCP


Mass: 58595.879 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: CUBANE CLUSTER [4FE-4S], HYBRID CLUSTER [4FE-3S], [4FE-3S-3O]
Source: (natural) DESULFOVIBRIO DESULFURICANS (bacteria) / References: UniProt: Q01770

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Non-polymers , 5 types, 1684 molecules

#2: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S4
#3: Chemical ChemComp-SF3 / FE4-S3 CLUSTER


Mass: 319.575 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S3
#4: Chemical ChemComp-FSO / IRON/SULFUR/OXYGEN HYBRID CLUSTER


Mass: 367.573 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4O3S3
#5: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1677 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsFUNCTION: CATALYZES REDUCTION OF HYDROXYLAMINE TO NH3 + H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.03 Å3/Da / Density % sol: 39 %
Crystal growTemperature: 279 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 25% PEG 8000, 0.1M MES PH6.0, TEMPERATURE 279 KELVIN, pH 6.00
Crystal grow
*PLUS
Temperature: 279 K / pH: 7.6 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
125 %PEG80001reservoir
20.1 MMES1reservoirpH6.0
312.6 mg/mlprotein1drop
420 mMTris-HCl1droppH7.6
50.2 M1dropNaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: May 1, 2000 / Details: TOROIDAL MIRROR
RadiationMonochromator: DIAMOND (111) CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.15→30 Å / Num. obs: 280898 / % possible obs: 84.8 % / Redundancy: 2.3 % / Biso Wilson estimate: 6.1 Å2 / Rmerge(I) obs: 0.082 / Net I/σ(I): 3.6
Reflection shellResolution: 1.15→1.19 Å / Redundancy: 1.3 % / Rmerge(I) obs: 0.271 / Mean I/σ(I) obs: 1.3 / % possible all: 70
Reflection
*PLUS
Highest resolution: 1.15 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.082
Reflection shell
*PLUS
% possible obs: 70 % / Redundancy: 1.3 % / Rmerge(I) obs: 0.271 / Mean I/σ(I) obs: 1.3

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Processing

Software
NameClassification
REFMACrefinement
DENZOdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1E2U

1e2u


Resolution: 1.25→27.52 Å / SU B: 0.606 / SU ML: 0.026 / Cross valid method: THROUGHOUT / ESU R: 0.043 / ESU R Free: 0.042 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.153 2141 1 %RANDOM
Rwork0.14 ---
obs0.14 227130 88.94 %-
Displacement parametersBiso mean: 8.521 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2---0.01 Å2-0.01 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.25→27.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8222 0 62 1677 9961
Refinement
*PLUS
Rfactor Rfree: 0.153 / Rfactor Rwork: 0.14
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONbond_d0.008
X-RAY DIFFRACTIONangle_d
X-RAY DIFFRACTIONangle_deg1.351
X-RAY DIFFRACTIONplane_restr0.005
X-RAY DIFFRACTIONchiral_restr0.147
LS refinement shell
*PLUS
Highest resolution: 1.25 Å / Lowest resolution: 1.29 Å / Rfactor Rfree: 0.221 / Num. reflection Rfree: 125 / Rfactor Rwork: 0.206 / Num. reflection Rwork: 13493

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