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- PDB-3mxu: Crystal structure of glycine cleavage system protein H from Barto... -

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Basic information

Entry
Database: PDB / ID: 3mxu
TitleCrystal structure of glycine cleavage system protein H from Bartonella henselae
ComponentsGlycine cleavage system H protein
KeywordsOXIDOREDUCTASE / Seattle Structural Genomics Center for Infectious Disease / SSGCID / Cat-scratch disease / bacteremia / lymphadenopathy / endocarditis / HIV co-infection
Function / homology
Function and homology information


glycine cleavage complex / glycine decarboxylation via glycine cleavage system
Similarity search - Function
Glycine cleavage system H-protein, subgroup / Glycine cleavage system H-protein / Glycine cleavage system H-protein/Simiate / Glycine cleavage H-protein / 2-oxo acid dehydrogenase, lipoyl-binding site / 2-oxo acid dehydrogenases acyltransferase component lipoyl binding site. / RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain / Biotinyl/lipoyl domain profile. / Biotin/lipoyl attachment / Single hybrid motif ...Glycine cleavage system H-protein, subgroup / Glycine cleavage system H-protein / Glycine cleavage system H-protein/Simiate / Glycine cleavage H-protein / 2-oxo acid dehydrogenase, lipoyl-binding site / 2-oxo acid dehydrogenases acyltransferase component lipoyl binding site. / RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain / Biotinyl/lipoyl domain profile. / Biotin/lipoyl attachment / Single hybrid motif / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
CITRIC ACID / Glycine cleavage system H protein
Similarity search - Component
Biological speciesBartonella henselae (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To be Published
Title: Crystal structure of glycine cleavage system protein H from Bartonella henselae
Authors: Edwards, T.E. / Gardberg, A.S. / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
History
DepositionMay 7, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 26, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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: Glycine cleavage system H protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,1485
Polymers15,7011
Non-polymers4464
Water2,810156
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Glycine cleavage system H protein
hetero molecules

A: Glycine cleavage system H protein
hetero molecules

A: Glycine cleavage system H protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,44315
Polymers47,1043
Non-polymers1,33912
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area6040 Å2
ΔGint-97 kcal/mol
Surface area18070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.910, 98.910, 131.540
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-124-

SO4

21A-124-

SO4

31A-149-

HOH

41A-161-

HOH

51A-167-

HOH

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Components

#1: Protein Glycine cleavage system H protein /


Mass: 15701.367 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bartonella henselae (bacteria) / Gene: gcvH, BH12830 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6G2F0
#2: Chemical ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 156 / 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: 3.94 Å3/Da / Density % sol: 68.81 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4
Details: 0.1 M sodium citrate pH 4.0, 0.8 M ammonium citrate, 25% ethylene glycol as cryo-protectant, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: May 6, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→35.9 Å / Num. obs: 23036 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 5 % / Biso Wilson estimate: 26.894 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 20.95
Reflection shellResolution: 1.8→1.85 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.557 / Mean I/σ(I) obs: 2.2 / Num. measured obs: 4804 / Num. unique obs: 1664 / % possible all: 98.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 55.01 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3 Å40.72 Å
Translation3 Å40.72 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HGB

3hgb


Resolution: 1.8→35.893 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.944 / WRfactor Rfree: 0.172 / WRfactor Rwork: 0.155 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.881 / SU B: 3.77 / SU ML: 0.056 / SU R Cruickshank DPI: 0.087 / SU Rfree: 0.085 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.085 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.196 1179 5.1 %RANDOM
Rwork0.176 ---
obs0.177 22981 99.28 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 54.39 Å2 / Biso mean: 22.006 Å2 / Biso min: 8.76 Å2
Baniso -1Baniso -2Baniso -3
1-0.11 Å20.05 Å20 Å2
2--0.11 Å20 Å2
3----0.16 Å2
Refinement stepCycle: LAST / Resolution: 1.8→35.893 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1000 0 27 156 1183
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0221087
X-RAY DIFFRACTIONr_angle_refined_deg1.3491.9851495
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0295149
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.14627.44747
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.84515177
X-RAY DIFFRACTIONr_dihedral_angle_4_deg27.373151
X-RAY DIFFRACTIONr_chiral_restr0.0920.2174
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021823
X-RAY DIFFRACTIONr_mcbond_it0.7811.5687
X-RAY DIFFRACTIONr_mcangle_it1.49821107
X-RAY DIFFRACTIONr_scbond_it2.3123400
X-RAY DIFFRACTIONr_scangle_it3.7914.5380
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.258 87 -
Rwork0.281 1574 -
all-1661 -
obs--98.63 %
Refinement TLS params.Method: refined / Origin x: -2.0801 Å / Origin y: 15.7998 Å / Origin z: 46.6881 Å
111213212223313233
T0.0806 Å20.0139 Å2-0.0142 Å2-0.0172 Å20.02 Å2--0.0467 Å2
L0.5135 °2-0.089 °2-0.2814 °2-0.773 °20.2609 °2--0.7767 °2
S0.0008 Å °0.0105 Å °0.0144 Å °-0.09 Å °-0.0495 Å °0.0278 Å °-0.1188 Å °-0.0318 Å °0.0487 Å °

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