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- PDB-3es4: Crystal structure of Protein of unknown function (DUF861) with a ... -

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Entry
Database: PDB / ID: 3es4
TitleCrystal structure of Protein of unknown function (DUF861) with a RmlC-like cupin fold (17741406) from AGROBACTERIUM TUMEFACIENS str. C58 (Dupont) at 1.64 A resolution
Componentsuncharacterized protein DUF861 with a RmlC-like cupin fold
Keywordsstructural genomics / unknown function / 17741406 / Protein of unknown function (DUF861) with a RmlC-like cupin fold / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology(S)-ureidoglycine aminohydrolase, cupin domain / EutQ-like cupin domain / RmlC-like cupin domain superfamily / Jelly Rolls / RmlC-like jelly roll fold / Jelly Rolls / Sandwich / Mainly Beta / (S)-ureidoglycine aminohydrolase cupin domain-containing protein
Function and homology information
Biological speciesAgrobacterium tumefaciens str. C58 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.64 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of Protein of unknown function (DUF861) with a RmlC-like cupin fold (17741406) from AGROBACTERIUM TUMEFACIENS str. C58 (Dupont) at 1.64 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionOct 3, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 14, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
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
Revision 1.4Feb 1, 2023Group: Database references / Derived calculations / Category: database_2 / 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

Downloads & links

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Assembly

Deposited unit
A: uncharacterized protein DUF861 with a RmlC-like cupin fold
B: uncharacterized protein DUF861 with a RmlC-like cupin fold
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,25014
Polymers25,5322
Non-polymers71812
Water5,405300
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4260 Å2
ΔGint-17 kcal/mol
Surface area11710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.254, 95.254, 83.155
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Refine code: 6 / Auth seq-ID: 3 - 113 / Label seq-ID: 3 - 113

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein uncharacterized protein DUF861 with a RmlC-like cupin fold


Mass: 12765.805 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrobacterium tumefaciens str. C58 (bacteria)
Gene: 17741406, AGR_L_3519, Atu3045 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: A9CEL1
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 300 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

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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: 2.84 Å3/Da / Density % sol: 56.74 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 1.4M Na3Citrate, 0.1M HEPES pH 7.5, NANODROP, 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: 0.97921
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Aug 4, 2008 / Details: Flat collimating mirror, toroid focusing mirror
RadiationMonochromator: Double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97921 Å / Relative weight: 1
ReflectionResolution: 1.64→29.285 Å / Num. obs: 34348 / % possible obs: 99.5 % / Redundancy: 7.3 % / Biso Wilson estimate: 17.626 Å2 / Rmerge(I) obs: 0.084 / Rsym value: 0.084 / Net I/σ(I): 5.927
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.64-1.685.10.3712.11225824190.37194.3
1.68-1.736.10.3232.31499524780.32399.4
1.73-1.787.60.2772.71818724060.277100
1.78-1.837.60.2193.41802023640.219100
1.83-1.897.60.18441716822650.184100
1.89-1.967.60.1554.51664121940.155100
1.96-2.037.60.13451631221350.134100
2.03-2.127.60.125.71573820610.12100
2.12-2.217.70.116.11512319660.11100
2.21-2.327.60.1046.51420418580.104100
2.32-2.447.70.16.81380317930.1100
2.44-2.597.70.0947.11297916830.094100
2.59-2.777.70.0917.31219415840.091100
2.77-2.997.70.0837.81135114760.083100
2.99-3.287.60.0758.61027213470.075100
3.28-3.677.60.06310.5934712360.063100
3.67-4.237.50.05711.3805010750.057100
4.23-5.197.40.05511.968049200.055100
5.19-7.337.40.0728.851807030.072100
7.33-29.2857.30.06410.127963850.06498.9

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
SCALA3.2.5data scaling
PDB_EXTRACT3.006data extraction
MOSFLMdata reduction
SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 1.64→29.285 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.964 / Occupancy max: 1 / Occupancy min: 0.25 / SU B: 2.393 / SU ML: 0.042 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.073 / ESU R Free: 0.07
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: (1). HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. (2). A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN ...Details: (1). HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. (2). A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. (3). ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. (4). CL ION AND 1,2-ETHYLENE GLYCOL(EDO) FROM EITHER CRYSTALLIZATION BUFFER OR CRYO SOLUTION WERE MODELED.
RfactorNum. reflection% reflectionSelection details
Rfree0.16 1735 5.1 %RANDOM
Rwork0.142 ---
obs0.143 34317 99.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 64.6 Å2 / Biso mean: 19.806 Å2 / Biso min: 6.24 Å2
Baniso -1Baniso -2Baniso -3
1-0.3 Å20.15 Å20 Å2
2--0.3 Å20 Å2
3----0.45 Å2
Refinement stepCycle: LAST / Resolution: 1.64→29.285 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1758 0 45 300 2103
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0221958
X-RAY DIFFRACTIONr_bond_other_d0.0020.021340
X-RAY DIFFRACTIONr_angle_refined_deg1.6051.9912666
X-RAY DIFFRACTIONr_angle_other_deg0.86533282
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8825259
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.32224.47476
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.40815315
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4841512
X-RAY DIFFRACTIONr_chiral_restr0.0880.2294
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022231
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02369
X-RAY DIFFRACTIONr_nbd_refined0.1880.2343
X-RAY DIFFRACTIONr_nbd_other0.2130.21415
X-RAY DIFFRACTIONr_nbtor_refined0.1770.2932
X-RAY DIFFRACTIONr_nbtor_other0.0860.21115
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.180.2237
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3130.223
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3170.272
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1430.237
X-RAY DIFFRACTIONr_mcbond_it2.25531335
X-RAY DIFFRACTIONr_mcbond_other0.5073497
X-RAY DIFFRACTIONr_mcangle_it2.53252037
X-RAY DIFFRACTIONr_scbond_it2.613788
X-RAY DIFFRACTIONr_scangle_it3.8355629
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 1338 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
LOOSE POSITIONAL0.545
LOOSE THERMAL1.6810
LS refinement shellResolution: 1.64→1.683 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.217 113 -
Rwork0.184 2294 -
all-2407 -
obs--94.32 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.84840.1408-0.15320.43150.01560.2895-0.01670.02740.0112-0.06140.0315-0.0834-0.0220.0463-0.0149-0.01520.00290.0147-0.03110.0017-0.0196-8.977617.678542.1744
21.02420.40590.02990.62770.24360.63010.0352-0.06830.0864-0.0092-0.0550.1033-0.0015-0.10420.0199-0.02860.00540.0135-0.0162-0.004-0.0317-27.486213.294848.6654
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 115
2X-RAY DIFFRACTION2B0 - 115

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