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- PDB-3hlx: Crystal Structure of PqqC Active Site Mutant Y175F in Complex with PQQ -

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Basic information

Entry
Database: PDB / ID: 3hlx
TitleCrystal Structure of PqqC Active Site Mutant Y175F in Complex with PQQ
ComponentsPyrroloquinoline-quinone synthase
KeywordsOXIDOREDUCTASE / PqqC / PQQ biosynthesis / oxidase / complex / all helical
Function / homology
Function and homology information


pyrroloquinoline-quinone synthase activity / pyrroloquinoline-quinone synthase / 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 / molecular replacement / Resolution: 1.3 Å
AuthorsPuehringer, S. / Schwarzenbacher, R.
CitationJournal: Proteins / Year: 2010
Title: Structural studies of mutant forms of the PQQ-forming enzyme PqqC in the presence of product and substrate
Authors: Puehringer, S. / RoseFigura, J. / Metlitzky, M. / Toyama, H. / Klinman, J.P. / Schwarzenbacher, R.
History
DepositionMay 28, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 12, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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_ncs_dom_lim / 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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)61,07410
Polymers59,9742
Non-polymers1,1008
Water7,080393
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7110 Å2
ΔGint-63 kcal/mol
Surface area19920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.607, 116.775, 68.279
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21D
12A
22D

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111LEULEUASPASP3AA2 - 852 - 85
211LEULEUASPASP3DB2 - 852 - 85
121GLYGLYHISHIS4AA92 - 25592 - 255
221GLYGLYHISHIS4DB92 - 25592 - 255
112PQQPQQPQQPQQ1AC500
212PQQPQQPQQPQQ1DG500

NCS ensembles :
ID
1
2

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Components

#1: Protein Pyrroloquinoline-quinone synthase / PqqC / 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: MGH 78578 / Gene: pqqC / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
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.: 4 / 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.: 393 / 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: 2.38 Å3/Da / Density % sol: 48.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2M Ammonium sulfate, 0.1M BIS-TRIS pH 6.5, 25% w/v Polyethylene glycol 3350, vapor diffusion, sitting drop, temperature 293K

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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 / Date: May 7, 2008
RadiationMonochromator: DIAMOND / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.3→37.7 Å / Num. obs: 124411 / % possible obs: 88.4 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.188 / Rsym value: 0.173 / Net I/σ(I): 10.5 / Num. measured all: 802891
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.3-1.3730.8551.341217107020.73853.1
4.11-37.76.30.14426.12942647050.13298.6

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.5 Å37.72 Å
Translation2.5 Å37.72 Å

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.1data scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1OTV

1otv


Resolution: 1.3→37.7 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.949 / WRfactor Rfree: 0.219 / WRfactor Rwork: 0.179 / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.882 / SU B: 1.921 / SU ML: 0.035 / SU R Cruickshank DPI: 0.056 / SU Rfree: 0.055 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.056 / ESU R Free: 0.055 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.198 6232 5 %RANDOM
Rwork0.164 ---
obs0.165 124354 88.24 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 52.24 Å2 / Biso mean: 12.088 Å2 / Biso min: 4.59 Å2
Baniso -1Baniso -2Baniso -3
1--0.63 Å20 Å20 Å2
2---0.71 Å20 Å2
3---1.34 Å2
Refinement stepCycle: LAST / Resolution: 1.3→37.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4152 0 74 393 4619
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0214468
X-RAY DIFFRACTIONr_bond_other_d0.0020.023054
X-RAY DIFFRACTIONr_angle_refined_deg1.7081.9386105
X-RAY DIFFRACTIONr_angle_other_deg1.16237344
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7585552
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.68822.456228
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.10215725
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4471543
X-RAY DIFFRACTIONr_chiral_restr0.110.2630
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.025060
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021009
X-RAY DIFFRACTIONr_nbd_refined0.2420.2961
X-RAY DIFFRACTIONr_nbd_other0.2110.23046
X-RAY DIFFRACTIONr_nbtor_refined0.1830.22141
X-RAY DIFFRACTIONr_nbtor_other0.0830.21934
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1610.2223
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.6030.213
X-RAY DIFFRACTIONr_symmetry_vdw_other0.4880.256
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4940.225
X-RAY DIFFRACTIONr_mcbond_it1.8971.52948
X-RAY DIFFRACTIONr_mcbond_other0.8241.51042
X-RAY DIFFRACTIONr_mcangle_it2.37624211
X-RAY DIFFRACTIONr_scbond_it3.35832227
X-RAY DIFFRACTIONr_scangle_it4.3614.51871
X-RAY DIFFRACTIONr_rigid_bond_restr1.64339181
X-RAY DIFFRACTIONr_sphericity_free9.6073405
X-RAY DIFFRACTIONr_sphericity_bonded4.15537377
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION

Ens-IDNumberTypeRms dev position (Å)Weight position
1490TIGHT POSITIONAL0.090.05
12173MEDIUM POSITIONAL0.210.5
1657LOOSE POSITIONAL0.345
1490TIGHT THERMAL0.390.5
12173MEDIUM THERMAL0.952
1657LOOSE THERMAL1.5710
227TIGHT POSITIONAL0.020.05
227TIGHT THERMAL0.340.5
LS refinement shellResolution: 1.3→1.334 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.36 222 -
Rwork0.32 4716 -
all-4938 -
obs--47.95 %

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