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- PDB-4h09: Crystal structure of a leucine-rich repeat protein (EUBVEN_01088)... -

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Basic information

Entry
Database: PDB / ID: 4h09
TitleCrystal structure of a leucine-rich repeat protein (EUBVEN_01088) from Eubacterium ventriosum ATCC 27560 at 2.50 A resolution
ComponentsHypothetical leucine rich repeat protein
KeywordsPROTEIN BINDING / TWO LRR_5 DOMAINS / PF13306 FAMILY / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-BIOLOGY
Function / homology
Function and homology information


: / BspA type Leucine rich repeat region / CAP domain / Cysteine-rich secretory protein family / CAP superfamily / BspA type Leucine rich repeat region (6 copies) / Bacterial Ig-like domain (group 2) / Invasin/intimin cell-adhesion fragments / Bacterial Ig-like domain 2 / Bacterial Ig-like domain, group 2 ...: / BspA type Leucine rich repeat region / CAP domain / Cysteine-rich secretory protein family / CAP superfamily / BspA type Leucine rich repeat region (6 copies) / Bacterial Ig-like domain (group 2) / Invasin/intimin cell-adhesion fragments / Bacterial Ig-like domain 2 / Bacterial Ig-like domain, group 2 / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Alpha-Beta Horseshoe / Fibronectin type III superfamily / Leucine-rich repeat domain superfamily / Immunoglobulin-like fold / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / SCP-like protein
Similarity search - Component
Biological speciesEubacterium ventriosum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be Published
Title: Crystal structure of a hypothetical leucine rich repeat protein (EUBVEN_01088) from Eubacterium ventriosum ATCC 27560 at 2.50 A resolution (CASP Target)
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionSep 7, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 10, 2012Provider: 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
Revision 1.4Nov 6, 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 leucine rich repeat protein
B: Hypothetical leucine rich repeat protein
C: Hypothetical leucine rich repeat protein
D: Hypothetical leucine rich repeat protein
E: Hypothetical leucine rich repeat protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)210,68047
Polymers207,8975
Non-polymers2,78342
Water7,188399
1
A: Hypothetical leucine rich repeat protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,53615
Polymers41,5791
Non-polymers95714
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Hypothetical leucine rich repeat protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,0148
Polymers41,5791
Non-polymers4347
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Hypothetical leucine rich repeat protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,8906
Polymers41,5791
Non-polymers3105
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Hypothetical leucine rich repeat protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,28811
Polymers41,5791
Non-polymers70910
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Hypothetical leucine rich repeat protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,9527
Polymers41,5791
Non-polymers3726
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)105.513, 105.513, 361.567
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61
DetailsCRYSTAL PACKING ANALYSIS SUGGESTS THE ASSIGNMENT OF A MONOMER AS THE SIGNIFICANT OLIGOMERIZATION STATE.

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Components

#1: Protein
Hypothetical leucine rich repeat protein


Mass: 41579.320 Da / Num. of mol.: 5 / Fragment: UNP residues 33-410
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Eubacterium ventriosum (bacteria) / Gene: EUBVEN_01088 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): PB1 / References: UniProt: A5Z5V6
#2: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 38 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 399 / 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 33-410 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: 2.79 Å3/Da / Density % sol: 55.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.1M sodium citrate pH 5.6, 20% 2-propanol, 20% polyethylene glycol 4000, 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: 0.91837,0.97925
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
10.918371
20.979251
ReflectionResolution: 2.5→29.965 Å / Num. all: 78283 / Num. obs: 78283 / % possible obs: 99.9 % / Redundancy: 4 % / Biso Wilson estimate: 56.569 Å2 / Rsym value: 0.09 / Net I/σ(I): 9.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.5-2.563.90.631.22283757980.63100
2.56-2.643.90.5341.42221756410.534100
2.64-2.713.90.4271.82152454680.427100
2.71-2.83.90.352.22097553280.35100
2.8-2.8940.2962.62026651250.296100
2.89-2.993.90.2353.21985450270.235100
2.99-3.13.90.184.11913348560.18100
3.1-3.2340.1454.61822746080.145100
3.23-3.3740.1166.31755644360.116100
3.37-3.543.90.0927.61686342720.092100
3.54-3.7340.0796.31621040740.079100
3.73-3.953.90.0699.21497737940.069100
3.95-4.2340.0659.21437936400.065100
4.23-4.5640.0629.81327333470.062100
4.56-540.0610.11224830970.06100
5-5.5940.05910.51101127800.059100
5.59-6.4640.0610.5976324470.0699.9
6.46-7.9140.05810.4826020880.05899.8
7.91-11.183.90.0599.5637416170.05999.4
11.18-29.9653.90.04911.132788400.04993

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SOLVEphasing
SCALA3.3.20data scaling
BUSTER-TNT2.10.0refinement
MOSFLMdata reduction
BUSTER2.10.0refinement
RefinementMethod to determine structure: MAD / Resolution: 2.5→29.965 Å / Cor.coef. Fo:Fc: 0.9534 / Cor.coef. Fo:Fc free: 0.9344 / 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). POLYETHYLENE GLYCOL FRAGMENTS (PEG) FROM THE CRYSTALLIZATION BUFFER AND 1,2-ETHANEDIOL (EDO), USED AS A CRYOPROTECTANT, HAVE BEEN MODELED INTO THE STRUCTURE. 3). ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 4). NCS RESTRAINTS WERE APPLIED USING BUSTER'S LSSR RESTRAINT REPRESENTATION (-AUTONCS). 5). THE REFINEMENT WAS RESTRAINED AGAINST THE MAD PHASES.
RfactorNum. reflection% reflectionSelection details
Rfree0.2093 3933 5.03 %RANDOM
Rwork0.1759 ---
obs0.1775 78165 99.94 %-
Displacement parametersBiso max: 158.59 Å2 / Biso mean: 65.1717 Å2 / Biso min: 29.85 Å2
Baniso -1Baniso -2Baniso -3
1--2.7827 Å20 Å20 Å2
2---2.7827 Å20 Å2
3---5.5654 Å2
Refine analyzeLuzzati coordinate error obs: 0.397 Å
Refinement stepCycle: LAST / Resolution: 2.5→29.965 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14029 0 180 399 14608
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d6533SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes299HARMONIC2
X-RAY DIFFRACTIONt_gen_planes2095HARMONIC5
X-RAY DIFFRACTIONt_it14458HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion2081SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance15HARMONIC1
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact17456SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d14458HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg19594HARMONIC21.15
X-RAY DIFFRACTIONt_omega_torsion3.8
X-RAY DIFFRACTIONt_other_torsion2.59
LS refinement shellResolution: 2.5→2.56 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2354 199 3.44 %
Rwork0.2054 5584 -
all0.2065 5783 -
obs--99.94 %
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)
10.6140.59520.20012.5042-0.29021.7560.0810.076-0.3105-0.2721-0.0435-0.25350.32240.1276-0.03750.0964-0.0175-0.1759-0.23440.0008-0.043746.663652.8605-4.8063
21.91060.86420.84732.03610.68821.14670.1236-0.36920.23140.215-0.31160.6464-0.0032-0.29520.1880.045-0.08780.0161-0.2047-0.08210.0063.679953.2083-4.8065
31.9278-0.6493-0.28131.15610.83561.93480.04310.0949-0.0645-0.39440.1976-0.1345-0.38970.3513-0.24070.0813-0.04010.1419-0.1782-0.0866-0.115197.14427.333231.5674
41.78580.7094-1.26031.0074-0.4813.25070.072-0.23840.0630.08490.01030.05620.39220.1184-0.08230.082-0.0833-0.0524-0.1639-0.1064-0.194254.08396.36397.8931
50.8222-0.50010.04991.66510.07611.9435-0.061-0.16440.07020.29680.08310.09980.4387-0.1876-0.02210.02920.0476-0.145-0.12530.0255-0.129946.205669.536534.0097
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|0 - 405 }A0 - 405
2X-RAY DIFFRACTION2{ B|0 - 403 }B0 - 403
3X-RAY DIFFRACTION3{ C|0 - 404 }C0 - 404
4X-RAY DIFFRACTION4{ D|0 - 404 }D0 - 404
5X-RAY DIFFRACTION5{ E|33 - 405 }E33 - 405

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