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- PDB-4hcj: Crystal Structure of ThiJ/PfpI Domain Protein from Brachyspira mu... -

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Basic information

Entry
Database: PDB / ID: 4hcj
TitleCrystal Structure of ThiJ/PfpI Domain Protein from Brachyspira murdochii
ComponentsThiJ/PfpI domain protein
KeywordsHYDROLASE / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG / alpha-beta-alpha sandwich
Function / homology
Function and homology information


metal ion binding / cytoplasm
Similarity search - Function
: / DJ-1/PfpI / DJ-1/PfpI family / Class I glutamine amidotransferase (GATase) domain / Class I glutamine amidotransferase-like / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FORMIC ACID / ThiJ/PfpI domain protein
Similarity search - Component
Biological speciesBrachyspira murdochii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.12 Å
AuthorsKim, Y. / Bigelow, L. / Jedrzejczak, R. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal Structure of ThiJ/PfpI Domain Protein from Brachyspira murdochii
Authors: Kim, Y. / Bigelow, L. / Jedrzejczak, R. / Joachimiak, A.
History
DepositionSep 30, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 24, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software
Revision 1.2Oct 9, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_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: ThiJ/PfpI domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,2536
Polymers19,0991
Non-polymers1545
Water5,513306
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.799, 42.197, 66.366
Angle α, β, γ (deg.)90.00, 116.95, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-568-

HOH

21A-569-

HOH

31A-603-

HOH

41A-604-

HOH

51A-605-

HOH

61A-606-

HOH

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Components

#1: Protein ThiJ/PfpI domain protein


Mass: 19098.715 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brachyspira murdochii (bacteria) / Strain: DSM 12563 / Gene: Bmur_0257 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 magic / References: UniProt: D5U596
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 306 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.12 Å3/Da / Density % sol: 41.91 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M Magnesium Chloride, 0.1 M HEPES:NaOH pH 7.5, 25% (w/v) PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97937 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 6, 2012 / Details: mirrors
RadiationMonochromator: double crystal monochromator / Protocol: SAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97937 Å / Relative weight: 1
ReflectionResolution: 1.12→50 Å / Num. all: 56517 / Num. obs: 56517 / % possible obs: 92.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 7.34 Å2 / Rsym value: 0.092 / Net I/σ(I): 15
Reflection shellResolution: 1.12→1.14 Å / Redundancy: 2.2 % / Mean I/σ(I) obs: 5.8 / Num. unique all: 1598 / Rsym value: 0.231 / % possible all: 51.5

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000data collection
HKL-3000phasing
SHELXSphasing
MLPHAREphasing
RESOLVEmodel building
ARP/wARPmodel building
ahelx-97refinement
PHENIX(phenix.refine: 1.8.1_1161)refinement
HKL-3000data reduction
HKL-3000data scaling
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.12→22.277 Å / SU ML: 0.06 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 10.65 / Stereochemistry target values: ML
Details: NUMBER OF REFLECTIONS ARE APPROXIMATELY TWO TIMES OF THAT OF OBSERVED BECAUSE I+ AND I- WERE USED IN THE FINAL ROUNDS OF REFINEMENT TO MODEL SE ATOMS BETTER (ANOMALOUS SCATTERING).
RfactorNum. reflection% reflectionSelection details
Rfree0.127 5374 5.01 %random
Rwork0.116 ---
all0.116 107273 --
obs0.116 107273 88.96 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 13.01 Å2
Refinement stepCycle: LAST / Resolution: 1.12→22.277 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1296 0 7 306 1609
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081496
X-RAY DIFFRACTIONf_angle_d1.1652043
X-RAY DIFFRACTIONf_dihedral_angle_d13.089550
X-RAY DIFFRACTIONf_chiral_restr0.079231
X-RAY DIFFRACTIONf_plane_restr0.005275
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
1.12-1.13280.1691710.15671400147136
1.1328-1.14610.1762860.13621691177745
1.1461-1.16010.12191150.13151867198250
1.1601-1.17480.13471130.12042261237458
1.1748-1.19020.13051510.12262337248863
1.1902-1.20650.1381430.11722828297172
1.2065-1.22380.1241440.11062961310579
1.2238-1.2420.11182020.11213468367091
1.242-1.26140.12741920.11463608380096
1.2614-1.28210.12981870.108138684055100
1.2821-1.30420.12711730.102437923965100
1.3042-1.32790.13551660.099239044070100
1.3279-1.35350.11522000.098437463946100
1.3535-1.38110.10321960.100638714067100
1.3811-1.41110.11982030.097637463949100
1.4111-1.44390.11712230.10338124035100
1.4439-1.480.10881660.096138794045100
1.48-1.520.1281970.097637693966100
1.52-1.56480.11112020.096438214023100
1.5648-1.61520.1272270.097638284055100
1.6152-1.6730.11761890.101637883977100
1.673-1.73990.10862140.107337723986100
1.7399-1.81910.12422210.110937573978100
1.8191-1.91490.11832100.11043841405199
1.9149-2.03480.12432240.11283759398399
2.0348-2.19180.12412240.11333720394499
2.1918-2.41210.11881800.12353821400199
2.4121-2.76060.12782110.12753772398399
2.7606-3.4760.15941730.13063777395099
3.476-22.28160.14371710.14153435360690

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