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- PDB-4hyz: Crystal structure of a DUF3887 family protein (RUMGNA_01855) from... -

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Basic information

Entry
Database: PDB / ID: 4hyz
TitleCrystal structure of a DUF3887 family protein (RUMGNA_01855) from Ruminococcus gnavus ATCC 29149 at 2.25 A resolution
ComponentsUncharacterized protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / PF13026 family protein / DUF3887 / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homologyNuclear Transport Factor 2; Chain: A, - #590 / Domain of unknown function DUF3887 / Protein of unknown function (DUF3887) / Nuclear Transport Factor 2; Chain: A, / Prokaryotic membrane lipoprotein lipid attachment site profile. / Roll / Alpha Beta / DUF3887 domain-containing protein
Function and homology information
Biological speciesRuminococcus gnavus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.25 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a hypothetical protein (RUMGNA_01855) from Ruminococcus gnavus ATCC 29149 at 2.25 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionNov 14, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 9, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 24, 2014Group: Structure summary
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Feb 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)28,36922
Polymers26,8432
Non-polymers1,52620
Water1,928107
1
A: Uncharacterized protein
B: Uncharacterized protein
hetero molecules

A: Uncharacterized protein
B: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,73844
Polymers53,6864
Non-polymers3,05240
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_556-y,-x,-z+7/61
Buried area10850 Å2
ΔGint-311 kcal/mol
Surface area23540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.290, 66.290, 253.830
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein Uncharacterized protein


Mass: 13421.566 Da / Num. of mol.: 2 / Fragment: UNP residues 36-148
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ruminococcus gnavus (bacteria) / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): PB1 / References: UniProt: A7B2S7
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 107 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE CONSTRUCT (RESIDUES 37-149) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG ...THE CONSTRUCT (RESIDUES 37-149) 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: 3 Å3/Da / Density % sol: 58.98 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4
Details: 2.40M ammonium sulfate, 0.1M citric acid pH 4.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97871,0.97922,0.91837
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 28, 2012
Details: Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (horizontal focusing)
RadiationMonochromator: single crystal Si(111) bent / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.978711
20.979221
30.918371
ReflectionResolution: 2.25→29.377 Å / Num. all: 16696 / Num. obs: 16696 / % possible obs: 99.9 % / Redundancy: 11.1 % / Biso Wilson estimate: 43.423 Å2 / Rsym value: 0.103 / Net I/σ(I): 15
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.25-2.31100.8730.91187011910.873100
2.31-2.3711.50.7291.11349611750.729100
2.37-2.4412.20.6051.31361111120.605100
2.44-2.52120.5361.41325611060.536100
2.52-2.611.60.4361.81237210680.436100
2.6-2.6911.30.3632.11160610280.363100
2.69-2.7910.20.2682.91042010250.268100
2.79-2.910.80.1983.8104879680.198100
2.9-3.0311.90.1714.4113959540.171100
3.03-3.1811.90.1355.6105948890.135100
3.18-3.3511.60.1056.999718630.105100
3.35-3.5611.20.0858.290278040.085100
3.56-3.89.90.06510.778047870.065100
3.8-4.1112.10.0611.588377330.06100
4.11-4.511.50.05312.877026700.053100
4.5-5.0310.90.05113.268196240.051100
5.03-5.819.20.05911.551795610.059100
5.81-7.1211.20.0739.454984900.073100
7.12-10.069.50.04614.537373920.04699.9
10.06-29.3778.60.041621902560.0496.3

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SHELXphasing
SHARPphasing
SCALA3.3.20data scaling
BUSTER-TNT2.10.0refinement
MOSFLMdata reduction
SHELXDphasing
BUSTER2.10.0refinement
RefinementMethod to determine structure: MAD / Resolution: 2.25→29.377 Å / Cor.coef. Fo:Fc: 0.9447 / Cor.coef. Fo:Fc free: 0.9364 / Occupancy max: 1 / Occupancy min: 0.5 / Cross valid method: THROUGHOUT / σ(F): 0
Details: 1. 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 ...Details: 1. 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. 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 3. THE MAD PHASES WERE USED AS RESTRAINTS DURING REFINEMENT. 4.SULFATE (SO4) FROM THE CRYSTALLIZATION, GLYCEROL(GOL), USED AS A CRYOPROTECTANT, AND CHLORIDE FROM THE PURIFICATION BUFFER HAVE BEEN MODELED INTO THE STRUCTURE. 5. 4. NCS RESTRAINTS WERE APPLIED USING BUSTER'S LSSR RESTRAINT REPRESENTATION (-AUTONCS). 5.UNEXPLAINED DIFFERENCE DENSITY NEAR TYR 118 ON THE A AND B SUBUNITS WAS NOT MODELED.
RfactorNum. reflection% reflectionSelection details
Rfree0.2084 842 5.07 %RANDOM
Rwork0.1865 ---
obs0.1876 16601 99.96 %-
Displacement parametersBiso max: 132.06 Å2 / Biso mean: 51.5237 Å2 / Biso min: 21.13 Å2
Baniso -1Baniso -2Baniso -3
1--1.618 Å20 Å20 Å2
2---1.618 Å20 Å2
3---3.236 Å2
Refine analyzeLuzzati coordinate error obs: 0.315 Å
Refinement stepCycle: LAST / Resolution: 2.25→29.377 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1822 0 84 107 2013
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d914SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes59HARMONIC2
X-RAY DIFFRACTIONt_gen_planes265HARMONIC5
X-RAY DIFFRACTIONt_it1935HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion239SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2198SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d1935HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg2593HARMONIC21.06
X-RAY DIFFRACTIONt_omega_torsion3.74
X-RAY DIFFRACTIONt_other_torsion2.8
LS refinement shellResolution: 2.25→2.4 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.2277 152 5.23 %
Rwork0.1977 2757 -
all0.1992 2909 -
obs--99.96 %
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)
12.9009-1.2283-1.52423.54092.21143.8883-0.1701-0.0365-0.14880.33650.0488-0.28470.57940.21490.12130.01070.00880.056-0.09470.0145-0.102754.1434-30.5441136.941
22.8011-0.24381.62012.70520.90424.7257-0.1918-0.18880.3194-0.1948-0.26010.3419-0.6217-0.37970.452-0.03630.0244-0.1281-0.1575-0.11880.027221.6714-19.1341138.934
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 149
2X-RAY DIFFRACTION2B0 - 149

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