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- PDB-3b9z: Crystal structure of the Nitrosomonas europaea Rh protein complex... -

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Basic information

Entry
Database: PDB / ID: 3b9z
TitleCrystal structure of the Nitrosomonas europaea Rh protein complexed with carbon dioxide
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
CARBON DIOXIDE / Unknown ligand / Ammonium transporter family
Similarity search - Component
Biological speciesNitrosomonas europaea ATCC 19718 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / 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 1.5Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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)41,4125
Polymers40,7831
Non-polymers6294
Water5,783321
1
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)124,23715
Polymers122,3503
Non-polymers1,88612
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area14200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.434, 100.434, 143.467
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-448-

HOH

21A-669-

HOH

31A-729-

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-CO2 / CARBON DIOXIDE


Mass: 44.010 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CO2
#4: Chemical ChemComp-UNL / UNKNOWN LIGAND


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


Mass: 18.015 Da / Num. of mol.: 321 / 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: 3.41 Å3/Da / Density % sol: 63.98 %
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: BL9-1 / Wavelength: 0.91837 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 3, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91837 Å / Relative weight: 1
ReflectionResolution: 1.85→41.631 Å / Num. all: 46080 / Num. obs: 45094 / % possible obs: 97.9 % / Observed criterion σ(I): 2 / Redundancy: 3.4 % / Biso Wilson estimate: 17.744 Å2 / Rmerge(I) obs: 0.076 / Rsym value: 0.076 / Net I/σ(I): 7.48
Reflection shellResolution: 1.85→1.9 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.523 / Mean I/σ(I) obs: 1.6 / Num. unique all: 3309 / Rsym value: 0.425 / % possible all: 95.9

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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
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3B9Y

3b9y


Resolution: 1.85→41.631 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.95 / SU B: 1.845 / SU ML: 0.057 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.105 / ESU R Free: 0.094 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.179 2275 5 %RANDOM
Rwork0.166 ---
obs0.166 45092 97.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.102 Å2
Baniso -1Baniso -2Baniso -3
1-0.52 Å20.26 Å20 Å2
2--0.52 Å20 Å2
3----0.78 Å2
Refinement stepCycle: LAST / Resolution: 1.85→41.631 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2942 0 47 321 3310
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0223060
X-RAY DIFFRACTIONr_angle_refined_deg1.0021.9814183
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.2875412
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.70823.714105
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.5515477
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.7291510
X-RAY DIFFRACTIONr_chiral_restr0.070.2518
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022226
X-RAY DIFFRACTIONr_nbd_refined0.1820.21680
X-RAY DIFFRACTIONr_nbtor_refined0.2980.22202
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0760.2312
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1320.285
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.080.234
X-RAY DIFFRACTIONr_mcbond_it0.3521.52019
X-RAY DIFFRACTIONr_mcangle_it0.62623128
X-RAY DIFFRACTIONr_scbond_it0.62631189
X-RAY DIFFRACTIONr_scangle_it0.9584.51042
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.24 192 -
Rwork0.232 3117 -
all-3309 -
obs--95.91 %

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