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- PDB-4ny7: Bond length analysis of the PqqC Y175F mutant structure shows evi... -

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Basic information

Entry
Database: PDB / ID: 4ny7
TitleBond length analysis of the PqqC Y175F mutant structure shows evidence for bound PQQ in the reduced form
ComponentsPyrroloquinoline-quinone synthase
KeywordsOXIDOREDUCTASE / all helical
Function / homology
Function and homology information


pyrroloquinoline-quinone synthase / pyrroloquinoline-quinone synthase activity / pyrroloquinoline quinone biosynthetic process / : / sulfur compound metabolic process
Similarity search - Function
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
PYRROLOQUINOLINE QUINONE / Pyrroloquinoline-quinone synthase
Similarity search - Component
Biological speciesKlebsiella pneumoniae subsp. pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.44 Å
AuthorsFisher, S.J. / Puehringer, S.
CitationJournal: To be Published
Title: Bond length analysis of the PqqC Y175F mutant structure shows evidence for bound PQQ in the reduced form
Authors: Fisher, S.J. / Puehringer, S.
History
DepositionDec 10, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 4, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pyrroloquinoline-quinone synthase
B: Pyrroloquinoline-quinone synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,62616
Polymers59,9742
Non-polymers1,65214
Water10,233568
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7890 Å2
ΔGint-68 kcal/mol
Surface area20260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.998, 116.020, 67.520
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Pyrroloquinoline-quinone synthase / Coenzyme PQQ synthesis protein C / Pyrroloquinoline quinone biosynthesis protein C


Mass: 29986.918 Da / Num. of mol.: 2 / Mutation: Y175F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae subsp. pneumoniae (bacteria)
Strain: ATCC 700721 / MGH 78578 / Gene: pqqC, KPN78578_17810, KPN_01811 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: A6T9H1, pyrroloquinoline-quinone synthase
#2: Chemical ChemComp-PQQ / PYRROLOQUINOLINE QUINONE


Mass: 330.206 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H6N2O8
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 568 / 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: 2.32 Å3/Da / Density % sol: 46.95 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.8
Details: 0.2M ammonium sulfate, 0.1M Bis-Tris pH 6.5, 25% w/v poly- ethylene glycol 3,350, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD
RadiationMonochromator: Diamond (111), Ge(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.43→37.72 Å / Num. all: 102022 / Num. obs: 100186 / % possible obs: 98.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.9 % / Rmerge(I) obs: 0.056 / Net I/σ(I): 21
Reflection shellResolution: 1.43→1.51 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.374 / Mean I/σ(I) obs: 4.3 / % possible all: 0.903

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Processing

Software
NameVersionClassification
MXCubedata collection
PHENIXmodel building
SHELXL-97refinement
XDSdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 3HLX

3hlx


Resolution: 1.44→10 Å / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.1821 4996 -RANDOM
obs0.1248 100065 97.7946 %-
all-102211 --
Refinement stepCycle: LAST / Resolution: 1.44→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4152 0 110 568 4830
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.0448
X-RAY DIFFRACTIONs_angle_d0.0382
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes
X-RAY DIFFRACTIONs_zero_chiral_vol
X-RAY DIFFRACTIONs_non_zero_chiral_vol
X-RAY DIFFRACTIONs_anti_bump_dis_restr
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt
X-RAY DIFFRACTIONs_similar_adp_cmpnt
X-RAY DIFFRACTIONs_approx_iso_adps

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