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- PDB-5byp: Crystal structure of an uncharacterized protein (BACEGG_01585) fr... -

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Basic information

Entry
Database: PDB / ID: 5byp
TitleCrystal structure of an uncharacterized protein (BACEGG_01585) from Bacteroides eggerthii DSM 20697 at 2.60 A resolution
ComponentsPutative uncharacterized protein
KeywordsUNKNOWN FUNCTION / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homologyLipocalin - #280 / Lipocalin / Beta Barrel / Mainly Beta / :
Function and homology information
Biological speciesBacteroides eggerthii DSM 20697 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.6 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of an uncharacterized protein (BACEGG_01585) from Bacteroides eggerthii DSM 20697 at 2.60 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJun 10, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 8, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Derived calculations / Refinement description / Source and taxonomy
Category: entity_src_gen / pdbx_struct_oper_list / software
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.2Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.3Feb 1, 2023Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative uncharacterized protein
B: Putative uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)29,7582
Polymers29,7582
Non-polymers00
Water00
1
A: Putative uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)14,8791
Polymers14,8791
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Putative uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)14,8791
Polymers14,8791
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)64.800, 64.800, 235.930
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122

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Components

#1: Protein Putative uncharacterized protein


Mass: 14879.056 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides eggerthii DSM 20697 (bacteria)
Gene: BACEGG_01585 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): PB1 / References: UniProt: B7AGQ7
Sequence detailsTHE CONSTRUCT (25-150) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...THE CONSTRUCT (25-150) 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: 2.08 Å3/Da / Density % sol: 40.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 3.5
Details: 34.00% polyethylene glycol 6000, 0.100M Sodium Iodide, 0.1M sodium citrate - citric acid pH 3.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97839,0.91837,0.9798
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 23, 2013
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
10.978391
20.918371
30.97981
ReflectionResolution: 2.6→42.712 Å / Num. obs: 8129 / % possible obs: 93.4 % / Observed criterion σ(I): -3 / Redundancy: 5.033 % / Biso Wilson estimate: 91.209 Å2 / Rmerge F obs: 0.999 / Rmerge(I) obs: 0.043 / Rrim(I) all: 0.047 / Net I/σ(I): 20.71 / Num. measured all: 73713
Reflection shell
Resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) allDiffraction-ID% possible all
2.55-2.640.7081.0541.2288515435841.175137.8
2.64-2.750.8290.7581.98091163316190.84699.1
2.75-2.870.9180.4693.27146148314660.52598.9
2.87-3.020.9770.2335.98326157415700.25899.7
3.02-3.210.9890.1499.88116156715630.16699.7
3.21-3.460.9970.08715.57540158915780.09799.3
3.46-3.80.9980.05325.17960154415370.05999.5
3.8-4.350.9990.03336.87943158115710.03799.4
4.35-5.460.9990.02945.37902155915560.03299.8
5.46-42.7120.9990.02649.37804161416030.02899.3

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassification
PDB_EXTRACT3.1data extraction
XDSdata scaling
XSCALEJanuary 10, 2014 BUILT=20140307data scaling
BUSTER-TNT2.10.0refinement
SHELXphasing
SHARPphasing
BUSTER2.10.0refinement
SHELXDphasing
RefinementMethod to determine structure: MAD / Resolution: 2.6→42.712 Å / Cor.coef. Fo:Fc: 0.909 / Cor.coef. Fo:Fc free: 0.8535 / Occupancy max: 1 / Occupancy min: 0.75 / 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.
RfactorNum. reflection% reflectionSelection details
Rfree0.2998 383 4.73 %RANDOM
Rwork0.2471 ---
obs0.2495 8104 98.95 %-
Displacement parametersBiso max: 174.16 Å2 / Biso mean: 95.0935 Å2 / Biso min: 58.91 Å2
Baniso -1Baniso -2Baniso -3
1--9.0707 Å20 Å20 Å2
2---9.0707 Å20 Å2
3---18.1415 Å2
Refine analyzeLuzzati coordinate error obs: 0.596 Å
Refinement stepCycle: LAST / Resolution: 2.6→42.712 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1957 0 0 0 1957
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d880SINUSOIDAL4
X-RAY DIFFRACTIONt_trig_c_planes51HARMONIC2
X-RAY DIFFRACTIONt_gen_planes296HARMONIC5
X-RAY DIFFRACTIONt_it2016HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion234SEMIHARMONIC5
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_contact2199SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2016HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg2725HARMONIC30.83
X-RAY DIFFRACTIONt_omega_torsion3.57
X-RAY DIFFRACTIONt_other_torsion2.53
LS refinement shellResolution: 2.6→2.91 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.3303 115 5.24 %
Rwork0.2562 2080 -
all0.26 2195 -
obs--98.95 %
Refinement TLS params.

T12: 0.152 Å2 / 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)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.4341-1.94420.76723.759-1.41293.46290.04340.54420.0419-0.4097-0.13820.24230.1337-0.54420.0948-0.304-0.01170.304-0.1238-0.304-8.285721.3437-11.0751
26.2612-0.3004-0.03573.614-0.32282.8753-0.30860.31980.5050.48010.0877-0.3893-0.0964-0.00520.2209-0.1287-0.06630.16340-0.206622.886110.4599-16.8491
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|30 - 150}A30 - 150
2X-RAY DIFFRACTION2{B|30 - 150}B30 - 150

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