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- PDB-1otv: PqqC, Pyrroloquinolinquinone Synthase C -

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Basic information

Entry
Database: PDB / ID: 1otv
TitlePqqC, Pyrroloquinolinquinone Synthase C
ComponentsCoenzyme PQQ synthesis protein C
KeywordsBIOSYNTHETIC PROTEIN / seven helix bundle / dimer / PQQ biosynthesis enzyme
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 synthase
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsMagnusson, O.T. / Toyama, H. / Saeki, M. / Rojas, A. / Reed, J.C. / Adachi, O. / Klinman, J.P. / SChwarzenbacher, R.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2004
Title: Quinone Biogenesis: Structure and Mechanism of PqqC, the Final Catalyst in the Production of Pyrroloquinoline Quinone.
Authors: Magnusson, O.T. / Toyama, H. / Saeki, M. / Rojas, A. / Reed, J.C. / Adachi, O. / Liddington, R.C. / Klinman, J.P. / Schwarzenbacher, R.
History
DepositionMar 23, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 11, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Jan 31, 2018Group: Advisory / Experimental preparation
Category: exptl_crystal_grow / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues
Item: _exptl_crystal_grow.temp
Revision 1.4Oct 27, 2021Group: Advisory / Database references
Category: database_2 / pdbx_unobs_or_zero_occ_atoms ...database_2 / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Remark 650author determined the secondary structure

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Coenzyme PQQ synthesis protein C
B: Coenzyme PQQ synthesis protein C


Theoretical massNumber of molelcules
Total (without water)60,2842
Polymers60,2842
Non-polymers00
Water2,342130
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4290 Å2
ΔGint-24 kcal/mol
Surface area23160 Å2
MethodPISA
2
A: Coenzyme PQQ synthesis protein C
B: Coenzyme PQQ synthesis protein C

A: Coenzyme PQQ synthesis protein C
B: Coenzyme PQQ synthesis protein C


Theoretical massNumber of molelcules
Total (without water)120,5684
Polymers120,5684
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area13210 Å2
ΔGint-58 kcal/mol
Surface area41700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.151, 118.127, 68.838
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
DetailsThe biological assembly is a dimer

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Components

#1: Protein Coenzyme PQQ synthesis protein C


Mass: 30142.113 Da / Num. of mol.: 2 / Mutation: A21D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: PQQC / Plasmid: pET101 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P27505
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 130 / 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: 2.51 Å3/Da / Density % sol: 50.68 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.8
Details: 1.4M ammonium sulphate, cacodylate , pH 6.8, VAPOR DIFFUSION, SITTING DROP, temperature 25K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.978 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 1, 2002
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.1→69 Å / Num. all: 35745 / Num. obs: 35743 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Biso Wilson estimate: 38.2 Å2 / Rsym value: 0.145 / Net I/σ(I): 10.1
Reflection shellResolution: 2.1→2.155 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 2.3 / Num. unique all: 1787 / Rsym value: 0.41 / % possible all: 96.2

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→69.01 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.936 / SU B: 4.518 / SU ML: 0.118 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.2 / ESU R Free: 0.17 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: Residues 152-160 of chain A and 151-162 of chain B are disordered, with an occupancy of 0. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23014 1787 5 %RANDOM
Rwork0.19489 ---
all0.19663 35745 --
obs0.19663 33956 99.18 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 32.916 Å2
Baniso -1Baniso -2Baniso -3
1--1.15 Å20 Å20 Å2
2---0.4 Å20 Å2
3---1.54 Å2
Refine analyzeLuzzati coordinate error obs: 0.136 Å
Refinement stepCycle: LAST / Resolution: 2.1→69.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4154 0 0 130 4284
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0214039
X-RAY DIFFRACTIONr_bond_other_d0.0020.023546
X-RAY DIFFRACTIONr_angle_refined_deg1.5881.9155477
X-RAY DIFFRACTIONr_angle_other_deg0.82638184
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0715483
X-RAY DIFFRACTIONr_chiral_restr0.0960.2568
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024551
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02908
X-RAY DIFFRACTIONr_nbd_refined0.230.3917
X-RAY DIFFRACTIONr_nbd_other0.2530.33904
X-RAY DIFFRACTIONr_nbtor_other0.0970.52130
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2210.5213
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2410.316
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3430.3118
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2820.535
X-RAY DIFFRACTIONr_mcbond_it1.72222418
X-RAY DIFFRACTIONr_mcangle_it2.91433847
X-RAY DIFFRACTIONr_scbond_it1.69821621
X-RAY DIFFRACTIONr_scangle_it2.67331630
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.304 137 -
Rwork0.26 2393 -
obs-1787 96.2 %
Refinement TLS params.Method: refined / Origin x: 33.957 Å / Origin y: 41.794 Å / Origin z: 17.269 Å
111213212223313233
T0.1027 Å20.0177 Å2-0.0143 Å2-0.026 Å20.0072 Å2--0.0178 Å2
L0.1426 °20.0302 °2-0.0918 °2--0.1913 °2-0.0404 °2--0.0163 °2
S0.0005 Å °-0.0773 Å °-0.1045 Å °-0.0029 Å °-0.0036 Å °0.0156 Å °0.031 Å °-0.005 Å °0.0031 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA4 - 2554 - 255
2X-RAY DIFFRACTION1BB - A4 - 2554 - 255

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