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- PDB-3dao: CRYSTAL STRUCTURE OF A PUTATIVE PHOSPHATE (EUBREC_1417) FROM EUBA... -

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Basic information

Entry
Database: PDB / ID: 3dao
TitleCRYSTAL STRUCTURE OF A PUTATIVE PHOSPHATE (EUBREC_1417) FROM EUBACTERIUM RECTALE AT 1.80 A RESOLUTION
ComponentsPutative Phosphate
KeywordsHYDROLASE / PUTATIVE PHOSPHATE / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-2
Function / homology
Function and homology information


Hypothetical Protein, Haloacid Dehalogenase-like Hydrolase; Chain: A; domain 2 - #10 / Cof family / Hypothetical Protein, Haloacid Dehalogenase-like Hydrolase; Chain: A; domain 2 / HAD-superfamily hydrolase, subfamily IIB / haloacid dehalogenase-like hydrolase / HAD superfamily/HAD-like / HAD superfamily / HAD-like superfamily / Rossmann fold / 2-Layer Sandwich ...Hypothetical Protein, Haloacid Dehalogenase-like Hydrolase; Chain: A; domain 2 - #10 / Cof family / Hypothetical Protein, Haloacid Dehalogenase-like Hydrolase; Chain: A; domain 2 / HAD-superfamily hydrolase, subfamily IIB / haloacid dehalogenase-like hydrolase / HAD superfamily/HAD-like / HAD superfamily / HAD-like superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
CITRIC ACID / HAD family hydrolase
Similarity search - Component
Biological speciesEubacterium rectale (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be Published
Title: Crystal structure of a Putative Phosphatase (RER070207001050) from Eubacterium rectale at 1.80 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionMay 29, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 29, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Jul 24, 2019Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: software / struct_conn / struct_ref_seq
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative Phosphate
B: Putative Phosphate
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,4754
Polymers65,0442
Non-polymers4302
Water12,250680
1
A: Putative Phosphate
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,7602
Polymers32,5221
Non-polymers2381
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Putative Phosphate
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,7142
Polymers32,5221
Non-polymers1921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)101.855, 101.855, 110.994
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
DetailsAUTHORS STATE THAT CRYSTAL PACKING ANALYSIS SUPPORTS THE ASSIGNMENT OF A MONOMER AS THE SIGNIFICANT OLIGOMERIZATION STATE.

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Components

#1: Protein Putative Phosphate /


Mass: 32522.088 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Eubacterium rectale (bacteria) / Gene: RER070207001050 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: D0VWU2*PLUS
#2: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 / Polyethylene glycol


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#3: Chemical ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 680 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG.

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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: 2.21 Å3/Da / Density % sol: 44.42 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.2000M NH4OAc, 30.0000% PEG-4000, 0.1M Citrate pH 5., NANODROP, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97915,0.97929,0.91162
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 2, 2008 / Details: Flat collimating mirror, toroid focusing mirror
RadiationMonochromator: Double crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979151
20.979291
30.911621
ReflectionResolution: 1.8→29.934 Å / Num. obs: 54677 / % possible obs: 100 % / Redundancy: 7.3 % / Biso Wilson estimate: 17.486 Å2 / Rmerge(I) obs: 0.114 / Rsym value: 0.114 / Net I/σ(I): 5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.8-1.857.30.5581.42911839690.558100
1.85-1.97.30.4531.72848938800.453100
1.9-1.957.30.37422778637840.374100
1.95-2.017.40.3012.52698536620.301100
2.01-2.087.30.25232623935700.252100
2.08-2.157.40.2143.52547234490.214100
2.15-2.237.40.18842446033210.188100
2.23-2.327.40.1734.22394532570.173100
2.32-2.437.40.1544.82267630770.154100
2.43-2.557.40.1325.42168629440.132100
2.55-2.687.30.11962077928290.119100
2.68-2.857.30.1076.31963826770.107100
2.85-3.047.30.0966.91833725070.096100
3.04-3.297.30.0857.61726023800.085100
3.29-3.67.20.0738.61571821700.073100
3.6-4.027.20.0689.11433719910.068100
4.02-4.657.10.0678.81261717800.067100
4.65-5.6970.0718.41051015110.071100
5.69-8.056.70.0797.4807812090.079100
8.05-29.9360.077.242827100.0798

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.4.0067refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
SCALAdata scaling
PDB_EXTRACT3.004data extraction
MOSFLMdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.8→29.934 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.943 / SU B: 2.34 / SU ML: 0.075 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.124 / ESU R Free: 0.12
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. CITRATE (CIT) AND PEG-4000 (1PE) MOLECULES FROM THE CRYSTALLIZATION/CRYO SOLUTIONS ARE MODELED.
RfactorNum. reflection% reflectionSelection details
Rfree0.208 2772 5.1 %RANDOM
Rwork0.168 ---
obs0.17 54610 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 16.944 Å2
Baniso -1Baniso -2Baniso -3
1-0.36 Å20 Å20 Å2
2--0.36 Å20 Å2
3----0.72 Å2
Refinement stepCycle: LAST / Resolution: 1.8→29.934 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4254 0 29 680 4963
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0224566
X-RAY DIFFRACTIONr_bond_other_d0.0020.023093
X-RAY DIFFRACTIONr_angle_refined_deg1.7391.9656231
X-RAY DIFFRACTIONr_angle_other_deg1.51937581
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6055591
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.39624.36211
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.43715779
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.3271524
X-RAY DIFFRACTIONr_chiral_restr0.1010.2687
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0215136
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02938
X-RAY DIFFRACTIONr_mcbond_it1.37522784
X-RAY DIFFRACTIONr_mcbond_other0.29621117
X-RAY DIFFRACTIONr_mcangle_it2.43944535
X-RAY DIFFRACTIONr_scbond_it4.08961782
X-RAY DIFFRACTIONr_scangle_it5.89881671
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.256 167 -
Rwork0.192 3800 -
all-3967 -
obs--100 %

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