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- PDB-3hxj: Crystal Structure of Pyrrolo-quinoline quinone (PQQ_DH) from Meth... -

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Basic information

Entry
Database: PDB / ID: 3hxj
TitleCrystal Structure of Pyrrolo-quinoline quinone (PQQ_DH) from Methanococcus maripaludis, Northeast Structural Genomics Consortium Target MrR86
ComponentsPyrrolo-quinoline quinone
KeywordsOXIDOREDUCTASE / All beta protein. Incomplete 8-blade beta-propeller. / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homology: / PQQ-like domain / Pyrrolo-quinoline quinone repeat / PQQ-like domain / Pyrrolo-quinoline quinone beta-propeller repeat / beta-propeller repeat / Quinoprotein alcohol dehydrogenase-like superfamily / WD40/YVTN repeat-like-containing domain superfamily / Pyrrolo-quinoline quinone
Function and homology information
Biological speciesMethanococcus maripaludis (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsForouhar, F. / Chen, Y. / Seetharaman, J. / Sahdev, S. / Xiao, R. / Ciccosanti, C. / Foote, E.L. / Zhao, L. / Everett, J.K. / Nair, R. ...Forouhar, F. / Chen, Y. / Seetharaman, J. / Sahdev, S. / Xiao, R. / Ciccosanti, C. / Foote, E.L. / Zhao, L. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Northeast Structural Genomics Consortium Target MrR86
Authors: Forouhar, F. / Chen, Y. / Seetharaman, J. / Sahdev, S. / Xiao, R. / Ciccosanti, C. / Foote, E.L. / Zhao, L. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G.T. / Hunt, J.F. / Tong, L.
History
DepositionJun 20, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 25, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.contact_author / _software.contact_author_email ..._software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pyrrolo-quinoline quinone
B: Pyrrolo-quinoline quinone
C: Pyrrolo-quinoline quinone
D: Pyrrolo-quinoline quinone
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,81311
Polymers149,1404
Non-polymers6727
Water12,052669
1
A: Pyrrolo-quinoline quinone
B: Pyrrolo-quinoline quinone
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,6663
Polymers74,5702
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3000 Å2
ΔGint-22 kcal/mol
Surface area25730 Å2
MethodPISA
2
C: Pyrrolo-quinoline quinone
D: Pyrrolo-quinoline quinone
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,1478
Polymers74,5702
Non-polymers5766
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3500 Å2
ΔGint-72 kcal/mol
Surface area25860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.225, 66.958, 112.082
Angle α, β, γ (deg.)90.000, 115.290, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Pyrrolo-quinoline quinone


Mass: 37285.074 Da / Num. of mol.: 4 / Mutation: L115M,P124T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanococcus maripaludis (archaea) / Strain: C7 / Gene: MmarC7 1297, MmarC7_1297 / Plasmid: BL21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+ Magic / References: UniProt: A6VIT4
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 669 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsIN ORDER TO DETERMINE THE CRYSTAL STRUCTURE OF THIS PROTEIN BY SAD PHASING USING SE-MET SIGNAL, LEU ...IN ORDER TO DETERMINE THE CRYSTAL STRUCTURE OF THIS PROTEIN BY SAD PHASING USING SE-MET SIGNAL, LEU 115 WAS MUTATED TO MET. RESIDUE 124 IS THR, NOT PRO BASED ON THE CURRENT CRYSTAL STRUCTURE, FOR THE ELECTRON DENSITY FOR THR IS UNAMBIGUOUS. THE PRESENT CRYSTAL STRUCTURE WAS OBTAINED BY CLONING A GENE FROM THE STRAIN DSM2067 (DEUTSCHE COLLECTION) OR ATCC 43000, WHOSE CLOSEST MATCH IS THE MMARC7_1297 GENE FROM METHANOCOCCUS MARIPALUDIS C7.

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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: 2.26 Å3/Da / Density % sol: 45.51 %
Crystal growTemperature: 291 K / Method: microbatch, under oil / pH: 5.5
Details: Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5), Reservoir solution: 0.1 M Bis-Tris (pH 5.5), 25% PEG3350, and 0.2 M Lithium sulfate, microbatch, under oil, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97905 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 31, 2009 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97905 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. all: 176293 / Num. obs: 173972 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 7.9 Å2 / Rmerge(I) obs: 0.067 / Rsym value: 0.058 / Net I/σ(I): 17.5
Reflection shellResolution: 2→2.07 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.281 / Mean I/σ(I) obs: 3 / Num. unique all: 17652 / Rsym value: 0.241 / % possible all: 89.2

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Processing

Software
NameVersionClassificationNB
CNS1.2 & XtalViewrefinement
PDB_EXTRACT3data extraction
MAR345dtbdata collection
DENZOdata reduction
SCALEPACKdata scaling
SnBthen SOLVE/RESOLVEphasing
REFMACrefinement
RefinementMethod to determine structure: SAD / Resolution: 2→19.98 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 219394.594 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.242 7581 5 %RANDOM
Rwork0.195 ---
all0.197 176288 --
obs0.196 151608 86 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 54.696 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 26.5 Å2
Baniso -1Baniso -2Baniso -3
1--2.49 Å20 Å2-2.29 Å2
2--1.94 Å20 Å2
3---0.55 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.21 Å0.14 Å
Refinement stepCycle: LAST / Resolution: 2→19.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9498 0 35 669 10202
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d26.6
X-RAY DIFFRACTIONc_improper_angle_d0.76
LS refinement shellResolution: 2→2.07 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.268 486 5 %
Rwork0.214 9195 -
obs-9681 54.9 %

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