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- PDB-3b9y: Crystal structure of the Nitrosomonas europaea Rh protein -

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Basic information

Entry
Database: PDB / ID: 3b9y
TitleCrystal structure of the Nitrosomonas europaea Rh protein
ComponentsAmmonium transporter family Rh-like protein
KeywordsTRANSPORT PROTEIN / carbon dioxide / channel / Rh protein / CO2
Function / homology
Function and homology information


ammonium homeostasis / ammonium channel activity / identical protein binding / plasma membrane
Similarity search - Function
Blood group Rhesus C/E/D polypeptide / Ammonium transporter fold / Ammonium transporter AmtB like domains / Ammonium transporter AmtB-like domain / Ammonium Transporter Family / Ammonium/urea transporter / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Unknown ligand / Ammonium transporter family
Similarity search - Component
Biological speciesNitrosomonas europaea ATCC 19718 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.85 Å
AuthorsLi, X. / Jayachandran, S. / Nguyen, H.-H.T. / Chan, M.K.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2007
Title: Structure of the Nitrosomonas europaea Rh protein.
Authors: Li, X. / Jayachandran, S. / Nguyen, H.H. / Chan, M.K.
History
DepositionNov 7, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.4Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Feb 21, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ammonium transporter family Rh-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,3684
Polymers40,7831
Non-polymers5853
Water6,233346
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A: Ammonium transporter family Rh-like protein
hetero molecules

A: Ammonium transporter family Rh-like protein
hetero molecules

A: Ammonium transporter family Rh-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,10512
Polymers122,3503
Non-polymers1,7549
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_445-y-1,x-y-1,z1
crystal symmetry operation3_545-x+y,-x-1,z1
Buried area14120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.438, 100.438, 143.875
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-447-

HOH

21A-667-

HOH

31A-703-

HOH

41A-705-

HOH

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Components

#1: Protein Ammonium transporter family Rh-like protein


Mass: 40783.473 Da / Num. of mol.: 1 / Fragment: Residues 31-418
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nitrosomonas europaea ATCC 19718 (bacteria)
Species: Nitrosomonas europaea / Strain: IFO 14298 / Gene: Rh50, NE0448 / Production host: Methylococcus capsulatus (bacteria) / References: UniProt: Q82X47
#2: Sugar ChemComp-BOG / octyl beta-D-glucopyranoside / Beta-Octylglucoside / octyl beta-D-glucoside / octyl D-glucoside / octyl glucoside


Type: D-saccharide / Mass: 292.369 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C14H28O6 / Comment: detergent*YM
IdentifierTypeProgram
b-octylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Chemical ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 1 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 346 / 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: 3.42 Å3/Da / Density % sol: 64.08 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 14.5% PEG 2000 MME, 1 mM EDTA, 0.1 M MES buffer, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.9794 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 3, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.85→41.631 Å / Num. all: 46212 / Num. obs: 46149 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Biso Wilson estimate: 19.2 Å2 / Rmerge(I) obs: 0.094 / Rsym value: 0.08 / Net I/σ(I): 7
Reflection shellResolution: 1.85→1.9 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.441 / Mean I/σ(I) obs: 2.2 / Num. unique all: 3404 / Rsym value: 0.373 / % possible all: 99.3

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0019refinement
PDB_EXTRACT3.004data extraction
Blu-Icedata collection
SCALAdata scaling
SHELXSphasing
RefinementMethod to determine structure: SAD / Resolution: 1.85→41.631 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.947 / SU B: 1.914 / SU ML: 0.06 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.1 / ESU R Free: 0.095 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.183 2339 5.1 %RANDOM
Rwork0.16 ---
obs0.161 46149 99.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.357 Å2
Baniso -1Baniso -2Baniso -3
1-0.17 Å20.09 Å20 Å2
2--0.17 Å20 Å2
3----0.26 Å2
Refinement stepCycle: LAST / Resolution: 1.85→41.631 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2942 0 44 346 3332
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0223058
X-RAY DIFFRACTIONr_angle_refined_deg0.9821.9814182
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.2325412
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.03423.714105
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.57315477
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.2681510
X-RAY DIFFRACTIONr_chiral_restr0.0690.2518
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022226
X-RAY DIFFRACTIONr_nbd_refined0.1810.21648
X-RAY DIFFRACTIONr_nbtor_refined0.2980.22198
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0740.2296
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1250.289
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.070.242
X-RAY DIFFRACTIONr_mcbond_it0.351.52021
X-RAY DIFFRACTIONr_mcangle_it0.62623128
X-RAY DIFFRACTIONr_scbond_it0.64631188
X-RAY DIFFRACTIONr_scangle_it0.9934.51041
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.273 175 -
Rwork0.226 3229 -
all-3404 -
obs--99.33 %

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