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- PDB-5vrc: Crystal structure for Methylobacterium extorquens PqqC (truncatio... -

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Basic information

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


pyrroloquinoline-quinone synthase / pyrroloquinoline-quinone synthase activity / 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 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)GM66569 (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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)127,3724
Polymers127,3724
Non-polymers00
Water1,51384
1
A: Bifunctional coenzyme PQQ synthesis protein C/D
C: 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 ...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., native gel electrophoresis, When expressed separately as independent proteins, both PqqD (truncation) and PqqC (truncation) run separately.
  • 63.7 kDa, 2 polymers
  • Search similar-shape structures of this assembly by Omokage search (details)
Theoretical massNumber of molelcules
Total (without water)63,6862
Polymers63,6862
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2060 Å2
ΔGint-18 kcal/mol
Surface area19390 Å2
MethodPISA
2
B: Bifunctional coenzyme PQQ synthesis protein C/D
D: Bifunctional coenzyme PQQ synthesis protein C/D


Theoretical massNumber of molelcules
Total (without water)63,6862
Polymers63,6862
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2130 Å2
ΔGint-16 kcal/mol
Surface area19850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.501, 114.185, 145.403
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 31843.119 Da / Num. of mol.: 4 / Fragment: C domain residues 1-260
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
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 84 / 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: 2.04 Å3/Da / Density % sol: 39.61 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop
Details: 500 microL well volumes. Drops suspended on siliconized glass. Protein solution: 8.0 mg/mL protein in buffer (50 mM Tris, pH 8.0, 200mM sodium chloride). Well solution: 100 mM HEPES, pH 8. ...Details: 500 microL well volumes. Drops suspended on siliconized glass. Protein solution: 8.0 mg/mL protein in buffer (50 mM Tris, pH 8.0, 200mM sodium chloride). Well solution: 100 mM HEPES, pH 8.07, 200 mM sodium chloride, and 23.75% w/v PEG-3350. All water used in well solution buffers was 0.55 mM sodium azide for fungal growth suppression. Protein:well solution was 1:1 (1 microL to 1 microL)

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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: Jul 18, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2→29.51 Å / Num. obs: 69169 / % possible obs: 97.8 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 14.4

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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→29.51 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.927 / SU B: 9.516 / SU ML: 0.122 / Cross valid method: THROUGHOUT / ESU R: 0.176 / ESU R Free: 0.159 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23634 3492 5.1 %RANDOM
Rwork0.19719 ---
obs0.19918 65610 97.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.9 Å2
Baniso -1Baniso -2Baniso -3
1-1.11 Å20 Å20 Å2
2--0.26 Å20 Å2
3----1.37 Å2
Refinement stepCycle: 1 / Resolution: 2→29.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6964 0 0 84 7048
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0280.0197151
X-RAY DIFFRACTIONr_bond_other_d0.0020.026430
X-RAY DIFFRACTIONr_angle_refined_deg2.4571.9389722
X-RAY DIFFRACTIONr_angle_other_deg1.448314677
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8115893
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.45722.194319
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.105151045
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.6781556
X-RAY DIFFRACTIONr_chiral_restr0.2410.21069
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.028079
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021641
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.9782.4573608
X-RAY DIFFRACTIONr_mcbond_other1.9782.4573607
X-RAY DIFFRACTIONr_mcangle_it2.8293.6694489
X-RAY DIFFRACTIONr_mcangle_other2.8293.6694490
X-RAY DIFFRACTIONr_scbond_it2.4092.7153543
X-RAY DIFFRACTIONr_scbond_other2.4092.7153544
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.6063.9725234
X-RAY DIFFRACTIONr_long_range_B_refined4.84429.2148284
X-RAY DIFFRACTIONr_long_range_B_other4.83829.28278
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.004→2.056 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.288 196 -
Rwork0.261 3553 -
obs--73.22 %
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)
10.79070.22560.12921.20180.5492.06420.05050.03030.1071-0.0702-0.00930.0459-0.1908-0.0961-0.04120.03180.0226-0.00030.0370.03150.1425-21.93279.4469-31.7764
20.59650.0550.02220.64660.00531.69240.02870.01520.06290.01670.00670.0284-0.2237-0.1456-0.03540.03260.01810.02240.0861-0.01830.1929-37.229413.40380.6663
31.11310.1376-0.25620.9162-0.43022.384-0.00230.0011-0.0271-0.0944-0.02450.03610.450400.02670.11160.0077-0.00960.003-0.00820.1254-20.535-16.8398-26.8734
41.11860.1583-0.58330.80710.17431.5549-0.0225-0.0761-0.06590.03620.0051-0.00910.22230.07060.01750.0397-0.00820.00380.08050.02850.1389-23.0999-8.83478.5129
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A14 - 257
2X-RAY DIFFRACTION2B15 - 258
3X-RAY DIFFRACTION3C15 - 258
4X-RAY DIFFRACTION4D16 - 258

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