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- PDB-3hml: Crystal Structure of PqqC Active Site Mutant H154S in Complex with PQQ -

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Basic information

Entry
Database: PDB / ID: 3hml
TitleCrystal Structure of PqqC Active Site Mutant H154S 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: 2.35 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 29, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 12, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 4, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.3Nov 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 / diffrn_source / 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 / _diffrn_source.pdbx_synchrotron_site / _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)60,5644
Polymers59,9042
Non-polymers6602
Water1,02757
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5210 Å2
ΔGint-29 kcal/mol
Surface area20460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.060, 118.291, 68.040
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 / PqqC / Coenzyme PQQ synthesis protein C / Pyrroloquinoline quinone biosynthesis protein C


Mass: 29951.848 Da / Num. of mol.: 2 / Mutation: H154S
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 57 / 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: 2.52 Å3/Da / Density % sol: 51.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 1.0M Ammonium sulfate, 0.1M HEPES pH 7.0, 0.5% w/v Polyethylene glycol 8000, vapor diffusion, sitting drop, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.8148 Å
DetectorType: MAR555 FLAT PANEL / Detector: IMAGE PLATE / Date: Oct 30, 2008
RadiationMonochromator: Ge triangular bent compressing 7 Fankuchen cut
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8148 Å / Relative weight: 1
ReflectionResolution: 2.35→39.44 Å / Num. obs: 25868 / % possible obs: 99.7 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.107 / Rsym value: 0.099 / Net I/σ(I): 13.6 / Num. measured all: 172549
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.35-2.485.30.8121.71942236400.73198.4
7.2-39.446.20.073657139230.06499.3

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.4 Å38.37 Å
Translation2.4 Å38.37 Å

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Processing

Software
NameVersionClassificationNB
SCALA3.2.25data scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1OTW

1otw


Resolution: 2.35→38.37 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.921 / WRfactor Rfree: 0.25 / WRfactor Rwork: 0.208 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.805 / SU B: 15.963 / SU ML: 0.191 / SU R Cruickshank DPI: 0.356 / SU Rfree: 0.254 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.347 / ESU R Free: 0.252 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.261 1311 5.1 %RANDOM
Rwork0.212 ---
obs0.215 25842 99.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 86.38 Å2 / Biso mean: 46.347 Å2 / Biso min: 23.47 Å2
Baniso -1Baniso -2Baniso -3
1--0.31 Å20 Å20 Å2
2---0.03 Å20 Å2
3---0.35 Å2
Refinement stepCycle: LAST / Resolution: 2.35→38.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3856 0 48 57 3961
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0214049
X-RAY DIFFRACTIONr_angle_refined_deg1.6961.9385505
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5975471
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.30822.749211
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.90515644
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0591537
X-RAY DIFFRACTIONr_chiral_restr0.1070.2565
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023177
X-RAY DIFFRACTIONr_nbd_refined0.210.21853
X-RAY DIFFRACTIONr_nbtor_refined0.30.22719
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1590.2155
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2090.231
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1660.211
X-RAY DIFFRACTIONr_mcbond_it0.9491.52449
X-RAY DIFFRACTIONr_mcangle_it1.53323780
X-RAY DIFFRACTIONr_scbond_it2.12132032
X-RAY DIFFRACTIONr_scangle_it3.0714.51722
LS refinement shellResolution: 2.35→2.411 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.445 88 -
Rwork0.325 1700 -
all-1788 -
obs--95.77 %

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