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- PDB-4z7r: The 1.98-angstrom crystal structure of Zn(2+)-bound PqqB from Met... -

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Basic information

Entry
Database: PDB / ID: 4z7r
TitleThe 1.98-angstrom crystal structure of Zn(2+)-bound PqqB from Methylobacterium extorquens
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 / 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 speciesMethylobacterium extorquens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.982 Å
AuthorsTu, X. / Wilmot, C.M.
CitationJournal: To Be Published
Title: Crystal structures reveal metal-binding plasticity at active site of PqqB
Authors: Tu, X. / Wimot, C.M.
History
DepositionApr 7, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 20, 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.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Coenzyme PQQ synthesis protein B
B: Coenzyme PQQ synthesis protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,6596
Polymers64,3972
Non-polymers2624
Water4,234235
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4390 Å2
ΔGint-82 kcal/mol
Surface area20680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.431, 51.991, 120.536
Angle α, β, γ (deg.)90.000, 95.490, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A and segid A
21chain B and segid B

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain A and segid AA0
211chain B and segid BB0

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Components

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


Mass: 32198.502 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methylobacterium extorquens (strain ATCC 14718 / DSM 1338 / AM1) (bacteria)
Strain: ATCC 14718 / DSM 1338 / AM1 / Gene: pqqB, pqqG, MexAM1_META1p1750 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q49149
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 235 / 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: 2.2 Å3/Da / Density % sol: 44.1 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.7 / Details: 20% PEG8000, 0.2M NaCl, Bis-Tris Propane pH7.0

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Data collection

DiffractionMean temperature: 108 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Feb 22, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.98→50 Å / Num. obs: 38935 / % possible obs: 99.4 % / Redundancy: 3 % / Biso Wilson estimate: 15.52 Å2 / Rmerge(I) obs: 0.115 / Rpim(I) all: 0.078 / Rrim(I) all: 0.14 / Χ2: 1.865 / Net I/av σ(I): 12.631 / Net I/σ(I): 9.3 / Num. measured all: 117845
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.98-2.012.10.4518600.7060.3660.5821.55596.9
2.01-2.052.20.41919210.720.3340.5381.62398.5
2.05-2.092.40.3619120.7450.2790.4571.74698.6
2.09-2.132.60.35619080.7810.2690.4481.60599.4
2.13-2.182.70.32819710.8090.2380.4071.68399.7
2.18-2.232.80.30319160.8540.2110.3711.62299.9
2.23-2.293.10.28419600.8890.1870.3422.83399.8
2.29-2.353.20.26519450.9110.1740.3181.661100
2.35-2.423.20.24719340.9250.1620.2961.737100
2.42-2.493.20.23419690.9210.1540.2811.733100
2.49-2.583.30.19819380.9520.130.2381.76299.9
2.58-2.693.20.16919400.9590.110.2021.652100
2.69-2.813.30.15519650.970.1010.1861.65599.9
2.81-2.963.30.13719400.9770.0890.1631.818100
2.96-3.143.30.10819610.9840.070.1291.71499.9
3.14-3.393.30.07919730.990.0510.0951.715100
3.39-3.733.40.06319770.9940.040.0751.92499.9
3.73-4.263.40.05219590.9950.0330.0612.02399.8
4.26-5.373.30.04619870.9950.030.0552.20699.7
5.37-5030.05519990.990.0380.0672.61996.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-3000data collection
SCALEPACKdata scaling
PHASER2.5.1phasing
PHENIXrefinement
PDB_EXTRACT3.15data extraction
HKL-3000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.982→21.788 Å / FOM work R set: 0.8589 / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2212 1956 5.03 %
Rwork0.1748 36958 -
obs0.1771 38914 99.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 200.45 Å2 / Biso mean: 15.85 Å2 / Biso min: 4.6 Å2
Refinement stepCycle: final / Resolution: 1.982→21.788 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4363 0 4 235 4602
Biso mean--21.03 27.09 -
Num. residues----578
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034445
X-RAY DIFFRACTIONf_angle_d0.7946051
X-RAY DIFFRACTIONf_chiral_restr0.03702
X-RAY DIFFRACTIONf_plane_restr0.003794
X-RAY DIFFRACTIONf_dihedral_angle_d12.4131611
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2512X-RAY DIFFRACTION4.369TORSIONAL
12B2512X-RAY DIFFRACTION4.369TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.982-2.03160.26271560.2182472262895
2.0316-2.08640.24671460.21112618276499
2.0864-2.14780.21961370.2052616275399
2.1478-2.21710.2671300.199226362766100
2.2171-2.29620.22641440.188226122756100
2.2962-2.3880.23041340.185526742808100
2.388-2.49660.27121320.179926372769100
2.4966-2.6280.22841450.175226332778100
2.628-2.79230.22381390.173226282767100
2.7923-3.00740.25041390.175127002839100
3.0074-3.30910.22191290.172426522781100
3.3091-3.78580.20171220.158527032825100
3.7858-4.76150.18541460.147926632809100
4.7615-21.78920.19621570.16642714287199
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.0964-0.0203-0.05890.1267-0.13880.2297-0.0110.02520.00260.02860.0218-0.0221-0.0457-0.0214-0.00020.08540.0036-0.00310.09490.00040.094951.2303-1.289721.4093
20.0156-0.0232-0.00410.02850.00790.0113-0.00210.0397-0.0441-0.02240.02580.0464-0.0734-0.12300.1502-0.0041-0.00690.16680.00780.155746.4176-1.44857.4624
30.05220.0199-0.05260.0124-0.04850.11820.00280.028-0.0074-0.06650.0322-0.00930.02790.00920.06410.0694-0.01280.00810.1177-0.00050.110458.7826-9.09164.6548
40.12850.14650.0810.2413-0.11450.3362-0.01350.0036-0.02260.06970.03140.02640.0264-0.02120.01330.09480.00870.01020.08190.00920.086249.4431-18.360938.3501
50.12740.10140.00340.1003-0.020.13710.0244-0.040.01910.20950.05130.0343-0.04630.02810.13430.18860.0259-0.00950.088900.094655.2719-8.314453.6374
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 164 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 165 through 193 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 194 through 299 )A0
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 207 )B0
5X-RAY DIFFRACTION5chain 'B' and (resid 208 through 299 )B0

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