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- PDB-4z5y: The 1.56-angstrom crystal structure of copper(II)-bound PqqB from... -

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Basic information

Entry
Database: PDB / ID: 4z5y
TitleThe 1.56-angstrom crystal structure of copper(II)-bound PqqB from Pseudomonas Putida
ComponentsCoenzyme PQQ synthesis protein B
KeywordsHYDROLASE / PqqB / PQQ / Pyrroloquinoline quinone / Pyrroloquinoline quinone B / metallo-beta-lactamase / beta-lactamase
Function / homology
Function and homology information


pyrroloquinoline quinone biosynthetic process
Similarity search - Function
Coenzyme PQQ biosynthesis protein B / : / Beta-lactamase superfamily domain / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase; Chain A / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
COPPER (II) ION / Coenzyme PQQ synthesis protein B
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.561 Å
AuthorsTu, X. / Wilmot, C.M.
CitationJournal: To Be Published
Title: Crystal structures reveal metal-binding plasticity at the active site of PqqB
Authors: Tu, X. / Wimot, C.M.
History
DepositionApr 3, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 13, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_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 B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,1374
Polymers33,9861
Non-polymers1523
Water4,630257
1
A: Coenzyme PQQ synthesis protein B
hetero molecules

A: Coenzyme PQQ synthesis protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,2758
Polymers67,9712
Non-polymers3046
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area4600 Å2
ΔGint-35 kcal/mol
Surface area22820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.202, 86.202, 106.625
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-620-

HOH

21A-755-

HOH

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Components

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


Mass: 33985.508 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: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 257 / 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: 2.91 Å3/Da / Density % sol: 57.79 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.7
Details: 11% PEG4000, 0.2M NaCl, 25 uM CuCl2, 0.1M Bis-Tris Propane

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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: Oct 30, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03 Å / Relative weight: 1
ReflectionResolution: 1.56→29.3 Å / Num. obs: 57676 / % possible obs: 99.9 % / Redundancy: 7.6 % / Biso Wilson estimate: 24.26 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.081 / Rpim(I) all: 0.032 / Net I/σ(I): 16.7 / Num. measured all: 438378
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
1.56-1.597.40.8122.82061327800.7870.31798.7
8.55-29.360.09227.625084190.9840.04197.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
Aimless0.3.11data scaling
PHASER2.5.1phasing
PHENIXrefinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.561→29.3 Å / FOM work R set: 0.913 / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 14.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1657 2928 5.08 %
Rwork0.1358 54663 -
obs0.1373 57591 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 72.24 Å2 / Biso mean: 32.19 Å2 / Biso min: 14.17 Å2
Refinement stepCycle: final / Resolution: 1.561→29.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2380 0 3 257 2640
Biso mean--32.42 41.59 -
Num. residues----308
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0122449
X-RAY DIFFRACTIONf_angle_d1.4563327
X-RAY DIFFRACTIONf_chiral_restr0.097358
X-RAY DIFFRACTIONf_plane_restr0.007446
X-RAY DIFFRACTIONf_dihedral_angle_d13.533902
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 21

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5607-1.58630.22971430.18112530267399
1.5863-1.61370.21031480.162425242672100
1.6137-1.6430.22451410.146525812722100
1.643-1.67460.19451450.138125492694100
1.6746-1.70880.17711300.125325742704100
1.7088-1.7460.18471390.116825602699100
1.746-1.78660.16391420.109425712713100
1.7866-1.83120.1561470.10825692716100
1.8312-1.88070.17711360.106725752711100
1.8807-1.93610.13771310.103525792710100
1.9361-1.99850.13281270.103826072734100
1.9985-2.070.16451380.107425752713100
2.07-2.15280.16221340.116826072741100
2.1528-2.25080.1491510.115825962747100
2.2508-2.36940.16861450.120925852730100
2.3694-2.51770.16251140.127926252739100
2.5177-2.7120.17241380.139626432781100
2.712-2.98470.16031400.140526402780100
2.9847-3.4160.15911570.143326352792100
3.416-4.30160.14371270.136927122839100
4.3016-29.30860.19031550.162528262981100

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