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- PDB-4z67: The 1.5-angstrom crystal structure of Mn(2+)-bound PqqB from Pseu... -

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Basic information

Entry
Database: PDB / ID: 4z67
TitleThe 1.5-angstrom crystal structure of Mn(2+)-bound PqqB from Pseudomonas Putida
ComponentsCoenzyme PQQ synthesis protein B
KeywordsHORMONE / PqqB / PQQ / metallo-beta-lactamase / beta-lactamase / Pyrroloquinoline quinone
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
D-MALATE / : / Coenzyme PQQ synthesis protein B
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.5 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. / Wilmot, 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)34,4015
Polymers34,1241
Non-polymers2774
Water5,729318
1
A: Coenzyme PQQ synthesis protein B
hetero molecules

A: Coenzyme PQQ synthesis protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,80210
Polymers68,2472
Non-polymers5558
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Buried area5770 Å2
ΔGint-60 kcal/mol
Surface area22280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.327, 86.327, 107.064
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-645-

HOH

21A-814-

HOH

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Components

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Protein , 1 types, 1 molecules A

#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

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Non-polymers , 5 types, 322 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-MLT / D-MALATE / (2R)-2-HYDROXYBUTANEDIOIC ACID / 2-HYDROXY-SUCCINIC ACID / Malic acid


Mass: 134.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O5
#4: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#5: Chemical ChemComp-NA / SODIUM ION


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


Mass: 18.015 Da / Num. of mol.: 318 / 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: 2.92 Å3/Da / Density % sol: 57.92 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.7
Details: 11% PEG4000, 0.2M NaCl, 1 mM MnCl2, 1 mM Malic acid, 0.1M Bis-Tris Propane pH6.7

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Data collection

DiffractionMean temperature: 108 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.987 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: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.5→29.35 Å / Num. obs: 65627 / % possible obs: 99.7 % / Redundancy: 8.6 % / Biso Wilson estimate: 19.86 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.065 / Rpim(I) all: 0.023 / Net I/σ(I): 19 / Num. measured all: 567404
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
1.5-1.524.60.9141.51410530670.4390.46496
8.2-29.357.90.03843.938054810.9990.01497.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
Aimless0.2.17data scaling
PHASER2.5.1phasing
PHENIXrefinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→29.35 Å / FOM work R set: 0.9072 / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 15.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1743 3325 5.07 %
Rwork0.1428 62227 -
obs0.1444 65552 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 66.42 Å2 / Biso mean: 26.45 Å2 / Biso min: 11.73 Å2
Refinement stepCycle: final / Resolution: 1.5→29.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2390 0 12 318 2720
Biso mean--23.87 40.64 -
Num. residues----309
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0162576
X-RAY DIFFRACTIONf_angle_d1.6023518
X-RAY DIFFRACTIONf_chiral_restr0.102375
X-RAY DIFFRACTIONf_plane_restr0.008478
X-RAY DIFFRACTIONf_dihedral_angle_d13.796958
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 24

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4963-1.51760.36371480.37022429257795
1.5176-1.54030.41651450.36425272672100
1.5403-1.56440.37891240.332125622686100
1.5644-1.590.28791480.262125562704100
1.59-1.61740.25751280.193125442672100
1.6174-1.64680.20761510.134325782729100
1.6468-1.67850.18021330.131525572690100
1.6785-1.71280.15841230.124725872710100
1.7128-1.750.15911370.118425772714100
1.75-1.79070.13951170.110625872704100
1.7907-1.83550.15421190.109525952714100
1.8355-1.88510.15651450.102625702715100
1.8851-1.94060.15491420.107725632705100
1.9406-2.00320.14141450.101725912736100
2.0032-2.07480.13521450.107725872732100
2.0748-2.15780.15111400.110725832723100
2.1578-2.2560.15811630.109325842747100
2.256-2.37490.15541430.119425902733100
2.3749-2.52360.18661240.131426172741100
2.5236-2.71830.16671280.139926472775100
2.7183-2.99160.18151490.145726332782100
2.9916-3.4240.16481520.152426232775100
3.424-4.31160.15981340.144627002834100
4.3116-29.35750.18671420.161128402982100

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