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- PDB-3g2b: crystal structure of PqqD from xanthomonas campestris -

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Basic information

Entry
Database: PDB / ID: 3g2b
Titlecrystal structure of PqqD from xanthomonas campestris
ComponentsCoenzyme PQQ synthesis protein D
KeywordsBIOSYNTHETIC PROTEIN / helix-turn-helix / PQQ biosynthesis
Function / homology
Function and homology information


pyrroloquinoline quinone biosynthetic process / quinone binding
Similarity search - Function
Coenzyme PQQ synthesis protein D (PqqD) / Coenzyme PQQ synthesis D, bacteria / Coenzyme PQQ synthesis protein D / Coenzyme PQQ synthesis protein D superfamily / Coenzyme PQQ synthesis protein D (PqqD) / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PHOSPHATE ION / PqqA binding protein
Similarity search - Component
Biological speciesXanthomonas campestris pv. campestris (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.66 Å
AuthorsYang, C.-Y. / Tsai, T.-Y.
CitationJournal: Proteins / Year: 2009
Title: Xanthomonas campestris PqqD in the pyrroloquinoline quinone biosynthesis operon adopts a novel saddle-like fold that possibly serves as a PQQ carrier
Authors: Tsai, T.-Y. / Yang, C.-Y. / Shih, H.-L. / Wang, A.H.-J. / Chou, S.-H.
History
DepositionJan 31, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 1, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Coenzyme PQQ synthesis protein D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,6792
Polymers10,5841
Non-polymers951
Water1,856103
1
A: Coenzyme PQQ synthesis protein D
hetero molecules

A: Coenzyme PQQ synthesis protein D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,3584
Polymers21,1682
Non-polymers1902
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_455-x-1,y,-z+1/21
Buried area5270 Å2
ΔGint-41 kcal/mol
Surface area10570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)26.900, 66.250, 93.880
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
DetailsAUTHOR DETERMINED BIOLOGICAL UNIT: UNKNOWN

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Components

#1: Protein Coenzyme PQQ synthesis protein D / Pyrroloquinoline quinone biosynthesis protein D


Mass: 10583.896 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthomonas campestris pv. campestris (bacteria)
Strain: 17 / Gene: pqqD / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8P6M8
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 103 / 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: 1.98 Å3/Da / Density % sol: 37.75 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 1.6M ammonium sulfate, 0.1M Tris pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 296K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 0.97907, 0.96370, 0.976
DetectorType: ADSC QUANTUM 315 / Detector: CCD
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979071
20.96371
30.9761
ReflectionResolution: 1.53→30 Å / Num. obs: 10203 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.6 % / Biso Wilson estimate: 22.1 Å2 / Net I/σ(I): 20.541
Reflection shellResolution: 1.53→1.58 Å / % possible all: 99.1

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Processing

Software
NameVersionClassification
HKL-2000data collection
SOLVEphasing
CNS1.2refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 1.66→19.5 Å / Occupancy max: 1 / Occupancy min: 1 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.228 529 5.1 %RANDOM
Rwork0.196 9448 --
obs-9977 96.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 45.722 Å2
Displacement parametersBiso max: 50.96 Å2 / Biso mean: 17.55 Å2 / Biso min: 7.53 Å2
Baniso -1Baniso -2Baniso -3
1-0.362 Å20 Å20 Å2
2--0.712 Å20 Å2
3----1.074 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.21 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.14 Å0.11 Å
Refinement stepCycle: LAST / Resolution: 1.66→19.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms709 0 5 103 817
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.175
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3po4_par.txtpo4_top.txt

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