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- PDB-4lr4: Crystal structure of a putative secreted protein (EUBREC_3654) fr... -

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Basic information

Entry
Database: PDB / ID: 4lr4
TitleCrystal structure of a putative secreted protein (EUBREC_3654) from Eubacterium rectale at 2.43 A resolution
Componentshypothetical protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / an orphan / two domains protein / N-terminus has a sandwich 10 strands in 2 sheets and jelly-roll fold / C -terminus has galactose-binding domain-like fold / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homologyJelly Rolls - #1420 / Jelly Rolls - #1430 / Jelly Rolls / Sandwich / Mainly Beta / PHOSPHATE ION / Uncharacterized protein
Function and homology information
Biological speciesEubacterium rectale (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.43 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a hypothetical protein (EUBREC_3654) from Eubacterium rectale at 2.43 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJul 19, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 18, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 24, 2014Group: Structure summary
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
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

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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
C: hypothetical protein
D: hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)167,70940
Polymers164,8754
Non-polymers2,83436
Water12,304683
1
A: hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,9079
Polymers41,2191
Non-polymers6898
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,7187
Polymers41,2191
Non-polymers4996
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,16313
Polymers41,2191
Non-polymers94412
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,92211
Polymers41,2191
Non-polymers70310
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)98.016, 106.733, 115.078
Angle α, β, γ (deg.)90.000, 92.450, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
hypothetical protein /


Mass: 41218.746 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Eubacterium rectale (bacteria) / Strain: ATCC 33656 / VPI 0990 / Gene: EUBREC_3654, RER070207000171 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): PB1 / References: UniProt: C4ZEB7
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: PO4
#4: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 683 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE CONSTRUCT (26-394) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...THE CONSTRUCT (26-394) 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: 3.65 Å3/Da / Density % sol: 66.28 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.83
Details: 1.5M ammonium dihydrogen phosphate, 20.0% Glycerol, 0.01M magnesium chloride, 0.1M TRIS pH 7.83, 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: 0.91837, 0.97864, 0.97805
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 2, 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
10.918371
20.978641
30.978051
ReflectionResolution: 2.43→48.963 Å / Num. obs: 87733 / % possible obs: 98.1 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 52.762 Å2 / Rmerge(I) obs: 0.102 / Net I/σ(I): 9.58
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.43-2.520.7771.931413908898.8
2.52-2.620.6632.128535848597.1
2.62-2.740.4443.129813872397.5
2.74-2.880.3633.930463852499.4
2.88-3.060.2325.630992879099.1
3.06-3.30.1458.330980889798.6
3.3-3.620.09511.527961835896.8
3.62-4.150.0616.831840896399
4.15-5.210.04620.528527864097
5.210.04521.630963903097.9

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SHELXphasing
SHARPphasing
XSCALEJuly 4, 2012data scaling
BUSTER-TNT2.10.0refinement
XDSdata reduction
SHELXDphasing
BUSTER2.10.0refinement
RefinementMethod to determine structure: MAD / Resolution: 2.43→48.963 Å / Cor.coef. Fo:Fc: 0.9314 / Cor.coef. Fo:Fc free: 0.9191 / 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. PHOSPHATE (PO4), GLYCEROL (GOL), AND CHLORIDE (CL) MODELED WERE PRESENT IN PROTEIN/CYRO CONDITIONS. 5.NCS RESTRAINTS WERE IMPOSED BY AUTOBUSTER'S LSSR PROCEDURE (-AUTONCS). 6. RAMACHANDRAN OUTLIERS (A,D/378, A-D/181) ARE SUPPORTED BY DENSITY.
RfactorNum. reflection% reflectionSelection details
Rfree0.2164 4383 5 %RANDOM
Rwork0.186 ---
obs0.1876 87703 98.23 %-
Displacement parametersBiso max: 179.94 Å2 / Biso mean: 52.857 Å2 / Biso min: 20.29 Å2
Baniso -1Baniso -2Baniso -3
1--14.7222 Å20 Å2-0.7022 Å2
2--3.7937 Å20 Å2
3---10.9285 Å2
Refine analyzeLuzzati coordinate error obs: 0.348 Å
Refinement stepCycle: LAST / Resolution: 2.43→48.963 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10779 0 161 683 11623
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d4924SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes291HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1608HARMONIC5
X-RAY DIFFRACTIONt_it11190HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1529SEMIHARMONIC5
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_contact12567SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d11190HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg15246HARMONIC21.07
X-RAY DIFFRACTIONt_omega_torsion3.44
X-RAY DIFFRACTIONt_other_torsion2.65
LS refinement shellResolution: 2.43→2.49 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.267 301 4.63 %
Rwork0.2324 6200 -
all0.2339 6501 -
obs--98.23 %
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)
10.64790.16140.06731.00511.07032.2545-0.04690.2078-0.1462-0.17450.01710.018-0.31730.00460.02980.0339-0.0064-0.0115-0.1565-0.0106-0.17431.530830.3291145.8418
20.9090.11380.73230.97451.11133.21690.0456-0.17750.05970.1976-0.1108-0.08240.46850.00770.0651-0.0398-0.0692-0.0099-0.19690.0184-0.17654.9852.671685.4229
30.4081-0.02380.18480.6346-0.43482.2673-0.03420.15390.11220.0096-0.02560.00120.05570.1520.05980.0191-0.0059-0.0106-0.12190.0077-0.124637.838133.996787.2565
40.8211-0.177-0.82441.13781.14262.78150.07010.1352-0.0911-0.1847-0.1241-0.0761-0.4067-0.08650.0539-0.00720.0724-0.0193-0.21210.0226-0.168553.78128.301188.1122
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|35 - 394}A35 - 394
2X-RAY DIFFRACTION2{B|35 - 394}B35 - 394
3X-RAY DIFFRACTION3{C|35 - 394}C35 - 394
4X-RAY DIFFRACTION4{D|35 - 394}D35 - 394

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