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- PDB-4eco: Crystal structure of a leucine-rich repeat protein (BACEGG_03329)... -

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Basic information

Entry
Database: PDB / ID: 4eco
TitleCrystal structure of a leucine-rich repeat protein (BACEGG_03329) from Bacteroides eggerthii DSM 20697 at 2.70 A resolution
ComponentsUncharacterized protein
KeywordsUNKNOWN FUNCTION / Leucine-rich repeats / protein binding / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homologyLeucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Alpha-Beta Horseshoe / Alpha Beta / :
Function and homology information
Biological speciesBacteroides eggerthii DSM 20697 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.7 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a hypothetical protein (BACEGG_03329) from Bacteroides eggerthii DSM 20697 at 2.70 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionMar 26, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 23, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 24, 2014Group: Structure summary
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Revision 1.3Feb 1, 2023Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)144,4203
Polymers144,3972
Non-polymers231
Water3,063170
1
A: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,2212
Polymers72,1981
Non-polymers231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)72,1981
Polymers72,1981
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)125.843, 193.663, 68.192
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Uncharacterized protein


Mass: 72198.281 Da / Num. of mol.: 2 / Fragment: UNP residues 270-904
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides eggerthii DSM 20697 (bacteria)
Gene: BACEGG_03329 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): PB1 / References: UniProt: B7AM07
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 170 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE CONSTRUCT (RESIDUES 270-904) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG ...THE CONSTRUCT (RESIDUES 270-904) 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: 2.88 Å3/Da / Density % sol: 57.25 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.20M NH4OAc, 30.00% PEG-4000, 0.1M Citrate pH 5.6, 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: 0.97899,0.91837
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 8, 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
10.978991
20.918371
ReflectionResolution: 2.7→48.416 Å / Num. obs: 45967 / % possible obs: 98.4 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 67.667 Å2 / Rmerge(I) obs: 0.085 / Net I/σ(I): 10.05
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
2.7-2.770.6211.8107113319197.4
2.77-2.850.4692.296453254198.2
2.85-2.930.3922.9113923239199.7
2.93-3.020.3373.3109213088199.6
3.02-3.120.2584.2108263079199.7
3.12-3.230.1875.8102732921199.6
3.23-3.350.15798492837199.2
3.35-3.490.1089.192792731199.1
3.49-3.640.0910.889252610199.1
3.64-3.820.07812.281972493198.1
3.82-4.020.06613.872342283194.6
4.02-4.270.05914.567642239197.9
4.27-4.560.05217.673822151199.7
4.56-4.930.04619.468401998199.4
4.93-5.40.05517.961721833198.5
5.4-6.040.05917.555381684198.8
6.04-6.970.05918.547061479197.7
6.97-8.540.05519.835591210192.2
8.54-12.070.0382633511009198.5
12.07-48.4160.02927.41789591194.4

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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
BUSTER-TNT2.10.0refinement
XDSdata reduction
SHELXDphasing
BUSTER2.10.0refinement
RefinementMethod to determine structure: MAD / Resolution: 2.7→48.416 Å / Cor.coef. Fo:Fc: 0.9398 / Cor.coef. Fo:Fc free: 0.8878 / 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. NCS RESTRAINTS WERE APPLIED USING BUSTER'S LSSR RESTRAINT REPRESENTATION (-AUTONCS). 5. THE SIDE-CHAIN IDENTITIES FOR 274-289 OF CHAIN A CANNOT BE IDENTIFIED UNAMBIGUOUSLY DUE TO POOR DENSITY. THUS THE REGION 274-289 MAY BE OUT OF REGISTER WITH ITS CORRECT POSITION IN THE ELECTRON DENSITY. 6. SODIUM ION MODELED WAS PRESENT IN THE CRYSTALLIZATION CONDITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.2174 2324 5.06 %RANDOM
Rwork0.1794 ---
obs0.1813 45922 98.44 %-
Displacement parametersBiso max: 149.59 Å2 / Biso mean: 57.4361 Å2 / Biso min: 21.18 Å2
Baniso -1Baniso -2Baniso -3
1--10.6411 Å20 Å20 Å2
2--10.6685 Å20 Å2
3----0.0274 Å2
Refine analyzeLuzzati coordinate error obs: 0.379 Å
Refinement stepCycle: LAST / Resolution: 2.7→48.416 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9694 0 1 170 9865
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d4697SINUSOIDAL4
X-RAY DIFFRACTIONt_trig_c_planes315HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1398HARMONIC5
X-RAY DIFFRACTIONt_it9945HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1313SEMIHARMONIC5
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_contact11531SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d9945HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg13472HARMONIC21.15
X-RAY DIFFRACTIONt_omega_torsion3.21
X-RAY DIFFRACTIONt_other_torsion2.76
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2987 170 5.17 %
Rwork0.239 3121 -
all0.2422 3291 -
obs--98.44 %
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)
10.379-0.136-0.01331.8253-0.06860.7565-0.07340.08120.01340.19430.11010.23990.0582-0.1197-0.0367-0.1407-0.03050.0412-0.0543-0.0131-0.1012149.74639.326833.8081
21.0429-0.07470.12391.7689-0.12870.8765-0.0063-0.03210.1958-0.33010.1234-0.42340.14770.1832-0.1171-0.14790.02620.0568-0.1384-0.0251-0.201107.55630.943269.9055
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A274 - 903
2X-RAY DIFFRACTION2B292 - 903

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