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- PDB-9kb4: The structure of the PpOngB-citrate -

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Basic information

Entry
Database: PDB / ID: 9kb4
TitleThe structure of the PpOngB-citrate
ComponentsCarbohydrate de-N-acetylated protein
KeywordsDE NOVO PROTEIN / metalloenzyme / carbohydrate deacetylase
Function / homologyCITRIC ACID
Function and homology information
Biological speciesPseudoalteromonas prydzensis ACAM 620 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsWang, J.P. / Li, P.Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, China) China
CitationJournal: To Be Published
Title: Structure of the complexes of PpOngB binding with citrate
Authors: Wang, J.P. / Wang, J.P.
History
DepositionOct 30, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Oct 8, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Carbohydrate de-N-acetylated protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,2883
Polymers53,0311
Non-polymers2582
Water10,178565
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)88.286, 88.286, 143.524
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z
Components on special symmetry positions
IDModelComponents
11A-727-

HOH

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Components

#1: Protein Carbohydrate de-N-acetylated protein


Mass: 53030.637 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudoalteromonas prydzensis ACAM 620 (bacteria)
Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 565 / 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: 3.04 Å3/Da / Density % sol: 59.6 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.5 M ammonium sulfate, 0.1 M sodium citrate tribasic dihydrate (pH 6.0) and 1.0 M lithium sulfate monohydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 2, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.85→67.48 Å / Num. obs: 54864 / % possible obs: 97.3 % / Redundancy: 1 % / CC1/2: 0.99 / Rmerge(I) obs: 0.115 / Net I/σ(I): 11.7
Reflection shellResolution: 1.85→1.95 Å / Num. unique obs: 59787 / CC1/2: 0.997 / % possible all: 91.4

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Processing

Software
NameVersionClassification
HKL-3000data collection
PDB_EXTRACTdata extraction
autoPROCdata processing
PHENIX1.17refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→52.32 Å / SU ML: 0.1561 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 18.0021
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1913 2735 4.99 %
Rwork0.1644 52062 -
obs0.1657 54797 97.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.37 Å2
Refinement stepCycle: LAST / Resolution: 1.85→52.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3650 0 14 565 4229
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00693739
X-RAY DIFFRACTIONf_angle_d0.84585086
X-RAY DIFFRACTIONf_chiral_restr0.0552577
X-RAY DIFFRACTIONf_plane_restr0.0068669
X-RAY DIFFRACTIONf_dihedral_angle_d7.0783508
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.880.26561220.22252226X-RAY DIFFRACTION83.03
1.88-1.910.25831160.20852297X-RAY DIFFRACTION87.65
1.91-1.950.22271260.18932424X-RAY DIFFRACTION92.79
1.95-1.990.24871470.18532568X-RAY DIFFRACTION97.66
1.99-2.030.22781220.17312687X-RAY DIFFRACTION99.89
2.03-2.080.19071530.16192626X-RAY DIFFRACTION100
2.08-2.130.19181550.16782609X-RAY DIFFRACTION100
2.13-2.190.2111320.162665X-RAY DIFFRACTION100
2.19-2.250.18121250.16932333X-RAY DIFFRACTION98.99
2.25-2.330.19811000.16172629X-RAY DIFFRACTION98.81
2.33-2.410.20411360.17112646X-RAY DIFFRACTION99.96
2.41-2.50.20961450.17432643X-RAY DIFFRACTION100
2.5-2.620.20451380.18622668X-RAY DIFFRACTION100
2.62-2.760.20521270.17352705X-RAY DIFFRACTION100
2.76-2.930.21141490.17982644X-RAY DIFFRACTION100
2.93-3.160.19051460.17342710X-RAY DIFFRACTION100
3.16-3.470.18361480.15812669X-RAY DIFFRACTION99.89
3.47-3.980.17991480.13732716X-RAY DIFFRACTION100
3.98-5.010.14681520.13372726X-RAY DIFFRACTION99.86
5.01-52.320.18061480.17272871X-RAY DIFFRACTION99.57

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