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- PDB-4z6x: The 1.68-angstrom crystal structure of acitive-site metal-free Pq... -

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Basic information

Entry
Database: PDB / ID: 4z6x
TitleThe 1.68-angstrom crystal structure of acitive-site metal-free PqqB from Pseudomonas putida
ComponentsCoenzyme PQQ synthesis protein B
KeywordsHYDROLASE / PqqB / PQQ / Pyrroloquinoline quinone / metallo-beta-lactamase / lactamase
Function / homology
Function and homology information


pyrroloquinoline quinone biosynthetic process
Similarity search - Function
Coenzyme PQQ biosynthesis protein B / Beta-lactamase superfamily domain / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase; Chain A / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Coenzyme PQQ synthesis protein B
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.68 Å
AuthorsTu, X. / Wilmot, C.M.
CitationJournal: To Be Published
Title: Crystal structures of PqqB reveal metal-binding plasticity at the active site of PqqB
Authors: Tu, X. / Wilmot, C.M.
History
DepositionApr 6, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 20, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Coenzyme PQQ synthesis protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,1892
Polymers34,1241
Non-polymers651
Water3,891216
1
A: Coenzyme PQQ synthesis protein B
hetero molecules

A: Coenzyme PQQ synthesis protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,3784
Polymers68,2472
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area4310 Å2
ΔGint-11 kcal/mol
Surface area23140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.694, 86.694, 106.871
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-621-

HOH

21A-716-

HOH

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Components

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


Mass: 34123.656 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (strain KT2440) (bacteria)
Strain: KT2440 / Gene: pqqB, PP_0379 / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(DE3) / References: UniProt: Q88QV5
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 216 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.92 Å3/Da / Density % sol: 57.87 %
Crystal growTemperature: 285 K / Method: vapor diffusion, hanging drop / pH: 6.7 / Details: PEG4000, NaCl, BisTris

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Data collection

DiffractionMean temperature: 108 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 22, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03 Å / Relative weight: 1
ReflectionResolution: 1.68→28.9 Å / Num. obs: 46746 / % possible obs: 99.4 % / Redundancy: 4.5 % / Biso Wilson estimate: 30.01 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.045 / Rpim(I) all: 0.023 / Net I/σ(I): 18.2 / Num. measured all: 211169
Reflection shell

Diffraction-ID: 1 / Redundancy: 4 % / Rejects: 0

Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
1.68-1.710.6022.3902422660.6710.33196.1
9.04-28.90.03535.813133260.9960.01990

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3JXP

3jxp


Resolution: 1.68→27.896 Å / FOM work R set: 0.9052 / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 15.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1753 2359 5.05 %Random selection
Rwork0.137 44334 --
obs0.1389 46693 99.25 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 163.17 Å2 / Biso mean: 43.11 Å2 / Biso min: 17.93 Å2
Refinement stepCycle: final / Resolution: 1.68→27.896 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2390 0 1 216 2607
Biso mean--33.18 48.27 -
Num. residues----309
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012491
X-RAY DIFFRACTIONf_angle_d1.2043391
X-RAY DIFFRACTIONf_chiral_restr0.056365
X-RAY DIFFRACTIONf_plane_restr0.005456
X-RAY DIFFRACTIONf_dihedral_angle_d14.169918
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 17

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6798-1.7140.22531290.17132500262997
1.714-1.75130.22761420.152525912733100
1.7513-1.7920.19891390.141125702709100
1.792-1.83680.21731440.132425792723100
1.8368-1.88650.18231440.12326062750100
1.8865-1.9420.17891420.112625852727100
1.942-2.00470.1671310.114325732704100
2.0047-2.07630.17231240.116726082732100
2.0763-2.15940.19661560.125625892745100
2.1594-2.25760.15761090.120526372746100
2.2576-2.37660.1551370.117726022739100
2.3766-2.52540.15241440.126125992743100
2.5254-2.72020.18061460.140926392785100
2.7202-2.99370.21241520.14912619277199
2.9937-3.42620.19421320.15462644277699
3.4262-4.31410.17351460.1352663280999
4.3141-27.90.15151420.14192730287296

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