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- PDB-4fvs: Crystal structure of a putative lipoprotein (BDI_3050) from Parab... -

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Basic information

Entry
Database: PDB / ID: 4fvs
TitleCrystal structure of a putative lipoprotein (BDI_3050) from Parabacteroides distasonis ATCC 8503 at 2.70 A resolution
Componentsputative lipoprotein
KeywordsLIPID BINDING PROTEIN / Putative exported protein with YMCC-like fold / DUF 3108 / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homologyYmcC-like fold - #20 / YmcC-like fold / Beta Barrel / Mainly Beta / Uncharacterized protein
Function and homology information
Biological speciesParabacteroides distasonis (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 putative lipoprotein (BDI_3050) from Parabacteroides distasonis ATCC 8503 at 2.70 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJun 29, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 25, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.2Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.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: putative lipoprotein
B: putative lipoprotein
C: putative lipoprotein
D: putative lipoprotein
E: putative lipoprotein
F: putative lipoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,33510
Polymers148,1936
Non-polymers1424
Water4,306239
1
A: putative lipoprotein


Theoretical massNumber of molelcules
Total (without water)24,6991
Polymers24,6991
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: putative lipoprotein


Theoretical massNumber of molelcules
Total (without water)24,6991
Polymers24,6991
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: putative lipoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,7703
Polymers24,6991
Non-polymers712
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: putative lipoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,7342
Polymers24,6991
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: putative lipoprotein


Theoretical massNumber of molelcules
Total (without water)24,6991
Polymers24,6991
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: putative lipoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,7342
Polymers24,6991
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)140.860, 154.510, 72.640
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
putative lipoprotein


Mass: 24698.867 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Parabacteroides distasonis (bacteria) / Strain: ATCC 8503 / Gene: BDI_3050 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): PB1 / References: UniProt: A6LGE3
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 239 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE CONSTRUCT (21-234) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...THE CONSTRUCT (21-234) 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: 2.67 Å3/Da / Density % sol: 53.88 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 9.5
Details: 20.0% polyethylene glycol 8000, 0.1M CHES pH 9.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.9785,0.9792,0.91162
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
10.97851
20.97921
30.911621
ReflectionResolution: 2.7→29.83 Å / Num. all: 44235 / Num. obs: 44235 / % possible obs: 99.8 % / Redundancy: 3.7 % / Rsym value: 0.079 / Net I/σ(I): 10.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.7-2.773.70.6641.11187132140.66499.9
2.77-2.853.70.5071.51167431400.50799.7
2.85-2.933.70.3971.91136630590.39799.7
2.93-3.023.70.3262.31103529740.32699.9
3.02-3.123.70.2423.11072628830.24299.8
3.12-3.233.70.1884.11040527930.18899.8
3.23-3.353.70.1335.71008127100.13399.8
3.35-3.493.70.1017.4960126000.10199.9
3.49-3.643.70.0838.9933125170.08399.9
3.64-3.823.70.0739.9888724090.073100
3.82-4.023.70.06511840922740.06599.9
4.02-4.273.70.05811.7800621770.058100
4.27-4.563.70.05112.8753020490.051100
4.56-4.933.70.04514.3700019110.045100
4.93-5.43.60.05212.5640417650.052100
5.4-6.043.60.06310.2582516140.06399.9
6.04-6.973.60.06310.3514014240.06399.9
6.97-8.543.60.05411.8437312240.05499.7
8.54-12.073.40.03816.933699790.03899.6
12.07-29.833.30.03617.916975190.03691.5

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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: 2.7→29.83 Å / Cor.coef. Fo:Fc: 0.9362 / Cor.coef. Fo:Fc free: 0.9155 / Occupancy max: 1 / Occupancy min: 0.3 / 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. CL IONS MODELED ARE PRESENT IN PROTEIN BUFFER.
RfactorNum. reflection% reflectionSelection details
Rfree0.2243 2228 5.04 %RANDOM
Rwork0.1872 ---
obs0.1891 44186 99.74 %-
Displacement parametersBiso max: 155.56 Å2 / Biso mean: 65.8897 Å2 / Biso min: 27.12 Å2
Baniso -1Baniso -2Baniso -3
1-12.971 Å20 Å20 Å2
2---4.839 Å20 Å2
3----8.1319 Å2
Refine analyzeLuzzati coordinate error obs: 0.402 Å
Refinement stepCycle: LAST / Resolution: 2.7→29.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10264 0 4 239 10507
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d4814SINUSOIDAL4
X-RAY DIFFRACTIONt_trig_c_planes346HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1490HARMONIC5
X-RAY DIFFRACTIONt_it10527HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1383SEMIHARMONIC5
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_contact11346SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d10527HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg14312HARMONIC21.11
X-RAY DIFFRACTIONt_omega_torsion3.28
X-RAY DIFFRACTIONt_other_torsion2.45
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2867 166 5.18 %
Rwork0.2298 3040 -
all0.2327 3206 -
obs--99.74 %
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)
13.2741-1.12140.37193.217-1.71163.69080.04670.24470.1781-0.3611-0.1638-0.17940.26470.14920.1171-0.156-0.0057-0.0549-0.17060.0263-0.0583-13.756361.162524.4106
20.87080.5832-0.20453.7817-1.1252.3659-0.1798-0.1216-0.27320.0139-0.1846-0.5442-0.0160.32030.3644-0.20030.01270.0743-0.06880.11660.020915.011334.1643-0.2532
33.6862-1.5943-0.36872.362-0.67532.91620.0368-0.1445-0.39780.18270.0315-0.0553-0.22560.0411-0.0683-0.1265-0.04740.0384-0.1424-0.0237-0.0566-51.038314.5710.6342
42.13490.2442-0.82162.75210.02942.5792-0.1519-0.3040.14990.5163-0.05250.23340.0572-0.12640.2044-0.14560.05270.0136-0.10030.0534-0.0007-6.737527.157534.544
52.4530.397-0.52630.5832-0.56491.8477-0.00890.4484-0.1062-0.0422-0.03890.2015-0.0102-0.1180.0478-0.13940.02320.0796-0.03990.01480.0643-15.77099.727511.4483
63.5707-1.7711.35411.6196-1.22613.4727-0.08350.0203-0.5442-0.020.17510.5442-0.0909-0.1099-0.0916-0.25740.02290.0356-0.17940.1360.152226.642712.905845.8821
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|21 - 234}A21 - 234
2X-RAY DIFFRACTION2{B|21 - 234}B21 - 234
3X-RAY DIFFRACTION3{C|21 - 234}C21 - 234
4X-RAY DIFFRACTION4{D|21 - 234}D21 - 234
5X-RAY DIFFRACTION5{E|22 - 234}E22 - 234
6X-RAY DIFFRACTION6{F|21 - 234}F21 - 234

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