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- PDB-9uai: Crystal structure of cyanobacterial CRD of CmpBCD in the presence... -

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Basic information

Entry
Database: PDB / ID: 9uai
TitleCrystal structure of cyanobacterial CRD of CmpBCD in the presence of nitrate
ComponentsNitrate transport ATP-binding subunits C and D
KeywordsTRANSPORT PROTEIN / ABC transporter / bicarbonate importer / membrane transporter / nitrate binding
Function / homologyNITRATE ION / :
Function and homology information
Biological speciesPseudanabaena sp. Chao 1811 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsLi, Q.Y. / Li, B. / Zhou, C.Z. / Jiang, Y.L.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Cryo-EM structure of cyanobacterial bicarbonate transporter CmpBCD
Authors: Li, Q.Y. / Li, B. / Zhou, C.Z. / Jiang, Y.L.
History
DepositionApr 1, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Apr 8, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
E: Nitrate transport ATP-binding subunits C and D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,5352
Polymers44,4731
Non-polymers621
Water4,828268
1
E: Nitrate transport ATP-binding subunits C and D
hetero molecules

E: Nitrate transport ATP-binding subunits C and D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,0694
Polymers88,9452
Non-polymers1242
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area2360 Å2
ΔGint-1 kcal/mol
Surface area27260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.271, 49.958, 97.585
Angle α, β, γ (deg.)90.00, 116.70, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Nitrate transport ATP-binding subunits C and D


Mass: 44472.555 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Sequence reference for strain 'Pseudanabaena sp. Chao 1811' is not available in UniProt at the time of biocuration. Current sequence reference is from UniProt id A0A2Z5WYP5.
Source: (gene. exp.) Pseudanabaena sp. Chao 1811 (bacteria) / Gene: nrtC, ABRG53_2086 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A2Z5WYP5
#2: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 268 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.27 Å3/Da / Density % sol: 45.87 %
Crystal growTemperature: 289.2 K / Method: vapor diffusion, sitting drop / Details: 12% PEG 20000, 0.1M Tris pH 8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: Cu FINE FOCUS / Wavelength: 1.5406 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Apr 18, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5406 Å / Relative weight: 1
ReflectionResolution: 1.75→13.07 Å / Num. obs: 40083 / % possible obs: 99.5 % / Redundancy: 3.6 % / CC1/2: 0.997 / Net I/σ(I): 11.3
Reflection shellResolution: 1.75→1.78 Å / Num. unique obs: 3967 / CC1/2: 0.489

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
HKL-2000data reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→13.07 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 24.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2294 1997 4.99 %
Rwork0.1969 --
obs0.1985 39993 99.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.75→13.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2919 0 0 268 3187
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082992
X-RAY DIFFRACTIONf_angle_d1.0264069
X-RAY DIFFRACTIONf_dihedral_angle_d5.688402
X-RAY DIFFRACTIONf_chiral_restr0.061445
X-RAY DIFFRACTIONf_plane_restr0.01531
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.790.34391260.32472681X-RAY DIFFRACTION99
1.79-1.840.27811460.28692673X-RAY DIFFRACTION99
1.84-1.90.30741550.262639X-RAY DIFFRACTION99
1.9-1.960.28761360.23372739X-RAY DIFFRACTION99
1.96-2.030.25291370.24192648X-RAY DIFFRACTION98
2.03-2.110.26841300.21752718X-RAY DIFFRACTION99
2.11-2.20.23061380.20662705X-RAY DIFFRACTION100
2.2-2.320.2381370.19612739X-RAY DIFFRACTION100
2.32-2.460.23821510.19532682X-RAY DIFFRACTION100
2.46-2.650.2261630.19332734X-RAY DIFFRACTION100
2.65-2.920.21191340.19592747X-RAY DIFFRACTION100
2.92-3.330.22641700.18682704X-RAY DIFFRACTION100
3.33-4.170.18521240.1582768X-RAY DIFFRACTION100
4.18-13.070.21500.17082819X-RAY DIFFRACTION100

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