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- PDB-5vrd: Crystal structure for Methylobacterium extorquens PqqCD (natural ... -

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Basic information

Entry
Database: PDB / ID: 5vrd
TitleCrystal structure for Methylobacterium extorquens PqqCD (natural fusion)
ComponentsBifunctional coenzyme PQQ synthesis protein C/D
KeywordsOXIDOREDUCTASE / PQQ / oxidase / alpha-helical bundle
Function / homology
Function and homology information


pyrroloquinoline-quinone synthase activity / pyrroloquinoline-quinone synthase / pyrroloquinoline quinone biosynthetic process / sulfur compound metabolic process / quinone binding
Similarity search - Function
Coenzyme PQQ synthesis D, bacteria / Coenzyme PQQ synthesis protein D / Coenzyme PQQ synthesis protein D superfamily / Coenzyme PQQ synthesis protein D (PqqD) / Coenzyme PQQ biosynthesis protein C / Pyrroloquinoline-quinone synthase-like / Thiaminase-2/PQQC / TENA/THI-4/PQQC family / Heme oxygenase-like / Heme Oxygenase; Chain A ...Coenzyme PQQ synthesis D, bacteria / Coenzyme PQQ synthesis protein D / Coenzyme PQQ synthesis protein D superfamily / Coenzyme PQQ synthesis protein D (PqqD) / Coenzyme PQQ biosynthesis protein C / Pyrroloquinoline-quinone synthase-like / Thiaminase-2/PQQC / TENA/THI-4/PQQC family / Heme oxygenase-like / Heme Oxygenase; Chain A / Haem oxygenase-like, multi-helical / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Bifunctional coenzyme PQQ synthesis protein C/D
Similarity search - Component
Biological speciesMethylobacterium extorquens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsEvans III, R.L. / Wilmot, C.M. / Esler, M.A.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM-66569 (C.M.W.) United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM-118117 (J.P.K.) United States
CitationJournal: Not published
Title: Crystal structures for Methylobacterium extorquens PqqC from the CD natural fusion and the C truncation
Authors: Evans III, R.L. / Esler, M.A. / Latham, J.A. / Klinman, J.P. / Wilmot, C.M.
History
DepositionMay 10, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 16, 2018Provider: repository / Type: Initial release
Revision 1.1May 29, 2019Group: Data collection / Database references / Category: citation / Item: _citation.journal_abbrev
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
D: Bifunctional coenzyme PQQ synthesis protein C/D
A: Bifunctional coenzyme PQQ synthesis protein C/D
B: Bifunctional coenzyme PQQ synthesis protein C/D
C: Bifunctional coenzyme PQQ synthesis protein C/D


Theoretical massNumber of molelcules
Total (without water)175,2064
Polymers175,2064
Non-polymers00
Water00
1
D: Bifunctional coenzyme PQQ synthesis protein C/D
B: Bifunctional coenzyme PQQ synthesis protein C/D


  • defined by author&software
  • Evidence: homology, PqqC is a physiological monomer in most species (few are naturally fused as Methylobacterium extorquens PqqCD is). This truncation from the CD natural fusion is monomeric like most independent PqqCs.
  • 87.6 kDa, 2 polymers
  • Search similar-shape structures of this assembly by Omokage search (details)
Theoretical massNumber of molelcules
Total (without water)87,6032
Polymers87,6032
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1820 Å2
ΔGint-17 kcal/mol
Surface area19590 Å2
MethodPISA
2
A: Bifunctional coenzyme PQQ synthesis protein C/D

C: Bifunctional coenzyme PQQ synthesis protein C/D


Theoretical massNumber of molelcules
Total (without water)87,6032
Polymers87,6032
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_455-y-1/2,x+1/2,z+1/41
Buried area1570 Å2
ΔGint-15 kcal/mol
Surface area20090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.936, 103.936, 243.485
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein
Bifunctional coenzyme PQQ synthesis protein C/D / Pyrroloquinoline quinone biosynthesis protein C/D


Mass: 43801.516 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methylobacterium extorquens (strain ATCC 14718 / DSM 1338 / JCM 2805 / NCIMB 9133 / AM1) (bacteria)
Strain: ATCC 14718 / DSM 1338 / JCM 2805 / NCIMB 9133 / AM1 / Gene: pqqCD, MexAM1_META1p1749 / Production host: Escherichia coli (E. coli)
References: UniProt: Q49150, pyrroloquinoline-quinone synthase

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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: 2.9 Å3/Da / Density % sol: 57.52 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop
Details: 500 microL well volumes. Protein solution: 8.0 mg/mL protein, 50 mM Tris, pH 7.9, 100 mM sodium chloride, and 1 mM TCEP. Well solution: 100 mM HEPES, pH 6.7, 19% w/v PEG-4000, 10% ...Details: 500 microL well volumes. Protein solution: 8.0 mg/mL protein, 50 mM Tris, pH 7.9, 100 mM sodium chloride, and 1 mM TCEP. Well solution: 100 mM HEPES, pH 6.7, 19% w/v PEG-4000, 10% isopropanol. Water used in the well solutions contained 0.55 mM sodium azide. Hanging drops were 1 microL protein solution and 1 microL well solution

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 19, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.85→243.49 Å / Num. obs: 31557 / % possible obs: 98.5 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.032 / Net I/σ(I): 17
Reflection shellRmerge(I) obs: 0.597 / Rpim(I) all: 0.32

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata scaling
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1otv

1otv


Resolution: 2.85→243.49 Å / Cor.coef. Fo:Fc: 0.914 / Cor.coef. Fo:Fc free: 0.854 / SU ML: 0.371 / Cross valid method: THROUGHOUT / ESU R: 0.995 / ESU R Free: 0.447 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.32707 1593 5.1 %RANDOM
Rwork0.25314 ---
obs0.2569 29899 98.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.09 Å20 Å20 Å2
2--1.09 Å20 Å2
3----2.17 Å2
Refinement stepCycle: 1 / Resolution: 2.85→243.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6570 0 0 0 6570
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0196723
X-RAY DIFFRACTIONr_bond_other_d0.0020.026220
X-RAY DIFFRACTIONr_angle_refined_deg2.0881.9419094
X-RAY DIFFRACTIONr_angle_other_deg1.241314247
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.1195796
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.88622.312333
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.46151091
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9391564
X-RAY DIFFRACTIONr_chiral_restr0.1190.2990
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.027425
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021547
X-RAY DIFFRACTIONr_mcbond_it3.6155.9843241
X-RAY DIFFRACTIONr_mcbond_other3.6135.9853240
X-RAY DIFFRACTIONr_mcangle_it5.648.9634018
X-RAY DIFFRACTIONr_mcangle_other5.6418.9634019
X-RAY DIFFRACTIONr_scbond_it3.4446.2473482
X-RAY DIFFRACTIONr_scbond_other3.4446.2473483
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.4969.2715077
X-RAY DIFFRACTIONr_long_range_B_refined8.50970.3337957
X-RAY DIFFRACTIONr_long_range_B_other8.50370.3237956
LS refinement shellResolution: 2.852→2.926 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.338 97 -
Rwork0.335 1817 -
obs--82.89 %
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)
11.35820.41620.04680.7923-0.12041.06090.1034-0.210.14720.0444-0.1863-0.0577-0.05420.04050.08290.2392-0.0516-0.01850.23190.01580.0389-36.6196.6068-20.8505
21.0019-0.72450.45351.2526-0.57120.8654-0.09620.24780.03490.0614-0.0318-0.12430.0570.11440.12810.15860.02510.02810.2485-0.01960.0306-35.1863-11.78815.7925
31.59910.76890.22931.123-0.22520.4698-0.07680.05760.2175-0.1562-0.05210.1188-0.13990.03910.12890.27710.0067-0.05570.14550.01850.0709-52.21616.1799-41.1781
41.00380.67070.34191.0910.58460.31790.2573-0.4366-0.040.14-0.31380.07750.0853-0.17930.05650.2727-0.1617-0.01050.33650.01950.0226-62.8479-17.6738-16.6281
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1D15 - 251
2X-RAY DIFFRACTION2A16 - 251
3X-RAY DIFFRACTION3B17 - 248
4X-RAY DIFFRACTION4C19 - 244

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