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- PDB-4o65: Crystal structure of the cupredoxin domain of amoB from Nitrosoca... -

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Basic information

Entry
Database: PDB / ID: 4o65
TitleCrystal structure of the cupredoxin domain of amoB from Nitrosocaldus yellowstonii
ComponentsPutative archaeal ammonia monooxygenase subunit B
KeywordsOXIDOREDUCTASE / Cupredoxin / ammonia monooxygenase / AMO / Ammonia oxidation / Ammonia / Membrane
Function / homology
Function and homology information


monooxygenase activity / metal ion binding
Similarity search - Function
Particulate methane monooxygenase, b subunit. Chain: A, domain 1 / Ammonia monooxygenase/particulate methane monooxygenase, subunit B / Ammonia/methane monooxygenase, subunitB, N-terminal / Monooxygenase subunit B protein / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
COPPER (II) ION / Putative archaeal ammonia monooxygenase subunit B
Similarity search - Component
Biological speciesCandidatus Nitrosocaldus yellowstonii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.796 Å
AuthorsLawton, T.J. / Ham, J. / Sun, T. / Rosenzweig, A.C.
CitationJournal: Proteins / Year: 2014
Title: Structural conservation of the B subunit in the ammonia monooxygenase/particulate methane monooxygenase superfamily.
Authors: Lawton, T.J. / Ham, J. / Sun, T. / Rosenzweig, A.C.
History
DepositionDec 20, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 2, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 3, 2014Group: Database references
Revision 1.2Nov 12, 2014Group: Structure summary
Revision 1.3Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative archaeal ammonia monooxygenase subunit B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,4124
Polymers18,1561
Non-polymers2563
Water2,972165
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)47.886, 47.886, 192.614
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-337-

HOH

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Components

#1: Protein Putative archaeal ammonia monooxygenase subunit B


Mass: 18156.414 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candidatus Nitrosocaldus yellowstonii (archaea)
Gene: amoB / Production host: Escherichia coli (E. coli) / References: UniProt: B0LKZ4
#2: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 165 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.04 Å3/Da / Density % sol: 59.55 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion / pH: 4
Details: 1 M NH4SO4, 100 mM sodium formate pH 4.0, and 2% polyethylene glycol 8000, VAPOR DIFFUSION, temperature 277.15K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 13, 2010
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.796→22.43 Å / Num. all: 20725 / Num. obs: 20852 / % possible obs: 99.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 1.796→7.842 Å / % possible all: 98.37

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Processing

Software
NameVersionClassification
HKL-2000data collection
SHARPphasing
REFMAC5.7.0032refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.796→22.43 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.932 / SU B: 4.041 / SU ML: 0.058 / Cross valid method: THROUGHOUT / ESU R: 0.099 / ESU R Free: 0.107 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.22874 1122 5.1 %RANDOM
Rwork0.18121 ---
obs0.18347 20724 99.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.035 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.796→22.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1188 0 11 165 1364
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.021225
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.21.9651665
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4545151
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.01524.07454
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.74315199
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.67158
X-RAY DIFFRACTIONr_chiral_restr0.2480.2185
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021928
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_it1.5541.558610
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.3552.322759
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.4012.168619
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined8.64516.0311907
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.796→1.842 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.253 76 -
Rwork0.212 1292 -
obs--98.13 %
Refinement TLS params.Method: refined / Origin x: -7.2447 Å / Origin y: -18.8341 Å / Origin z: 12.8149 Å
111213212223313233
T0.0239 Å2-0.0126 Å20.0126 Å2-0.1005 Å20.0037 Å2--0.0614 Å2
L0.9114 °20.0668 °20.1915 °2-0.1666 °20.2708 °2--0.4874 °2
S-0.0402 Å °-0.2046 Å °0.0302 Å °-0.026 Å °0.0141 Å °-0.0062 Å °-0.0195 Å °-0.0141 Å °0.0261 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A36 - 194
2X-RAY DIFFRACTION1A201 - 204
3X-RAY DIFFRACTION1A301 - 465

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