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- PDB-4gl6: Crystal structure of a DUF5037 family protein (RUMGNA_01148) from... -

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Basic information

Entry
Database: PDB / ID: 4gl6
TitleCrystal structure of a DUF5037 family protein (RUMGNA_01148) from Ruminococcus gnavus ATCC 29149 at 2.55 A resolution
Componentshypothetical protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / HYPOTHETICAL PROTEIN / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-BIOLOGY
Function / homologyDomain of unknown function (DUF5037), C-terminal subdomain / Domain of unknown function (DUF5037), N-terminal subdomain / Protein of unknown function DUF5037 / Domain of unknown function (DUF5037) / Diaminopimelate Epimerase; Chain A, domain 1 / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta / DUF5037 domain-containing protein
Function and homology information
Biological speciesRuminococcus gnavus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.55 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a hypothetical protein (RUMGNA_01148) from Ruminococcus gnavus ATCC 29149 at 2.55 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionAug 13, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 3, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 24, 2014Group: Structure summary
Revision 1.2Oct 11, 2017Group: Data collection / Refinement description / Category: reflns_shell / software
Item: _reflns_shell.percent_possible_all / _software.classification / _software.name
Revision 1.3Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.4Feb 1, 2023Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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 / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 20, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: hypothetical protein
B: hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,2305
Polymers57,9542
Non-polymers2763
Water46826
1
A: hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1613
Polymers28,9771
Non-polymers1842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0692
Polymers28,9771
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)148.653, 84.139, 53.031
Angle α, β, γ (deg.)90.000, 98.310, 90.000
Int Tables number5
Space group name H-MC121
DetailsCRYSTAL PACKING ANALYSIS SUGGESTS THE ASSIGNMENT OF A MONOMER AS THE SIGNIFICANT OLIGOMERIZATION STATE.

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Components

#1: Protein hypothetical protein


Mass: 28976.992 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ruminococcus gnavus (bacteria) / Strain: ATCC 29149 / Gene: RUMGNA_01148 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): PB1 / References: UniProt: A7B0S2
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHIS CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THIS CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY RESIDUES 25-270 OF 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: 2.83 Å3/Da / Density % sol: 56.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.08M sodium cacodylate pH 6.5, 20% glycerol, 16% polyethylene glycol 8000, 0.16M magnesium acetate, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.91162,0.97922
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 3, 2012 / Details: double crystal monochromator
RadiationMonochromator: double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.911621
20.979221
ReflectionResolution: 2.55→45.971 Å / Num. obs: 21164 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 62.923 Å2 / Rmerge(I) obs: 0.076 / Net I/σ(I): 12.84
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.55-2.640.7392.179422080100
2.64-2.750.5612.782862176100
2.75-2.870.36547721201999.6
2.87-3.020.2635.279712095100
3.02-3.210.1747.68076212299.8
3.21-3.460.10411.58050213499.7
3.46-3.80.06916.57893209299.9
3.8-4.350.04422.78034212299.9
4.35-5.460.039267913211699.7
5.460.039298067220899.3

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SHELXphasing
SHARPphasing
XSCALEDecember 29, 2011data scaling
REFMAC5.6.0117refinement
XDSdata reduction
SHELXDphasing
RefinementMethod to determine structure: MAD / Resolution: 2.55→45.971 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.939 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 22.894 / SU ML: 0.212 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.469 / ESU R Free: 0.251
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. 3. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 4. WATERS WERE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. 3. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 4. WATERS WERE EXCLUDED FROM AUTOMATIC TLS ASSIGNMENT. 5. 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 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 6. GLYCEROL (GOL) MOLECULES FROM THE CRYSTALLIZATION SOLUTION ARE MODELED.
RfactorNum. reflection% reflectionSelection details
Rfree0.218 1088 5.1 %RANDOM
Rwork0.1883 ---
obs0.1899 21159 99.72 %-
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 max: 187.75 Å2 / Biso mean: 61.0088 Å2 / Biso min: 30.27 Å2
Baniso -1Baniso -2Baniso -3
1-3.91 Å20 Å23.53 Å2
2---4.81 Å20 Å2
3---1.93 Å2
Refinement stepCycle: LAST / Resolution: 2.55→45.971 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3893 0 18 26 3937
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.024008
X-RAY DIFFRACTIONr_bond_other_d0.0040.022700
X-RAY DIFFRACTIONr_angle_refined_deg1.6461.9575415
X-RAY DIFFRACTIONr_angle_other_deg1.40436614
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.6085478
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.91626.318220
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.24515696
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.905156
X-RAY DIFFRACTIONr_chiral_restr0.0980.2547
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024507
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02783
LS refinement shellResolution: 2.55→2.616 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.353 79 -
Rwork0.333 1421 -
all-1500 -
obs--99.87 %
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)
12.8428-0.0154-0.5931.8870.46042.4383-0.0564-0.2568-0.2560.1769-0.1189-0.16940.21360.2090.17530.20030.0169-0.13950.30970.07320.1748.7713.9668.463
23.99480.99390.03062.35680.2431.61330.20210.04030.5524-0.0804-0.0898-0.1025-0.12290.0814-0.11230.18360.0602-0.05510.22960.00060.244453.66332.9430.57
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A28 - 264
2X-RAY DIFFRACTION2B0 - 264

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