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- PDB-9z6r: Crystal Structure of CBS domain containing protein from Burkholde... -

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Basic information

Entry
Database: PDB / ID: 9z6r
TitleCrystal Structure of CBS domain containing protein from Burkholderia phymatum
ComponentsCBS domain containing protein
KeywordsUNKNOWN FUNCTION / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE / CBS domain containing protein / Burkholderia phymatum
Function / homology: / Domain in cystathionine beta-synthase and other proteins. / CBS domain superfamily / CBS domain / CBS domain / CBS domain profile. / ACETATE ION / CBS domain containing protein
Function and homology information
Biological speciesParaburkholderia phymatum STM815 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.39 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)75N93022C00036 United States
National Institutes of Health/Office of the DirectorS10OD030394 United States
CitationJournal: To be published
Title: Crystal Structure of CBS domain containing protein from Burkholderia phymatum
Authors: Ung, A.R. / Lovell, S. / Battaile, K.P.
History
DepositionNov 14, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 26, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CBS domain containing protein
B: CBS domain containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,4646
Polymers28,1402
Non-polymers3244
Water2,810156
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, dimeric
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2490 Å2
ΔGint-26 kcal/mol
Surface area12500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.947, 40.742, 67.579
Angle α, β, γ (deg.)90.00, 93.11, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein CBS domain containing protein


Mass: 14070.085 Da / Num. of mol.: 2 / Fragment: 1-120
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paraburkholderia phymatum STM815 (bacteria)
Gene: Bphy_4760 / Plasmid: BuphA.00062.a.B2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B2JRV0
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 156 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.05 Å3/Da / Density % sol: 39.97 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: Berkeley A2: 100 mM sodium acetate, pH 4.5, 2 M sodium formate. BuphA.00062.a.B2.PW39454 at 37 mg/mL. plate 20515 A2 drop 2, Puck: PSL-0210, Cryo: 80% crystallant + 20% PEG 200

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.9786 Å
DetectorType: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Nov 1, 2025
RadiationMonochromator: Double Crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 1.39→41.89 Å / Num. obs: 46058 / % possible obs: 99.9 % / Redundancy: 6.7 % / CC1/2: 1 / Rmerge(I) obs: 0.032 / Rpim(I) all: 0.013 / Rrim(I) all: 0.035 / Χ2: 1.05 / Net I/σ(I): 21.5 / Num. measured all: 310724
Reflection shellResolution: 1.39→1.41 Å / % possible obs: 100 % / Redundancy: 6.1 % / Rmerge(I) obs: 0.97 / Num. measured all: 13692 / Num. unique obs: 2261 / CC1/2: 0.762 / Rpim(I) all: 0.424 / Rrim(I) all: 1.062 / Χ2: 1.03 / Net I/σ(I) obs: 1.7

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Processing

Software
NameVersionClassification
PHENIX2.0_5875refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.39→41.89 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1937 2391 5.2 %
Rwork0.1623 --
obs0.1641 46025 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.39→41.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1789 0 19 156 1964
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091893
X-RAY DIFFRACTIONf_angle_d1.0582586
X-RAY DIFFRACTIONf_dihedral_angle_d18.098751
X-RAY DIFFRACTIONf_chiral_restr0.078314
X-RAY DIFFRACTIONf_plane_restr0.011343
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.39-1.420.33041450.29042518X-RAY DIFFRACTION100
1.42-1.450.30571060.25562606X-RAY DIFFRACTION100
1.45-1.480.24331390.21642545X-RAY DIFFRACTION100
1.48-1.520.24361380.18072549X-RAY DIFFRACTION100
1.52-1.560.21351150.16052601X-RAY DIFFRACTION100
1.56-1.610.20421290.152550X-RAY DIFFRACTION100
1.61-1.660.20761380.1592552X-RAY DIFFRACTION100
1.66-1.720.18881490.16342563X-RAY DIFFRACTION100
1.72-1.790.2511500.1762543X-RAY DIFFRACTION100
1.79-1.870.22591590.16232523X-RAY DIFFRACTION100
1.87-1.970.18751550.14632538X-RAY DIFFRACTION100
1.97-2.090.19391330.14542607X-RAY DIFFRACTION100
2.09-2.250.17411060.14972612X-RAY DIFFRACTION100
2.25-2.480.18121450.15072548X-RAY DIFFRACTION100
2.48-2.840.19641670.16962551X-RAY DIFFRACTION100
2.84-3.570.21091350.16832610X-RAY DIFFRACTION99
3.57-41.890.17441820.15812618X-RAY DIFFRACTION99

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