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- PDB-3jx8: Crystal structure of Putative lipid binding protein (YP_001304415... -

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Basic information

Entry
Database: PDB / ID: 3jx8
TitleCrystal structure of Putative lipid binding protein (YP_001304415.1) from Parabacteroides distasonis ATCC 8503 at 2.16 A resolution
ComponentsPutative lipoprotein
KeywordsCELL ADHESION / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2 / Lipoprotein / Adhesin
Function / homologyPectate Lyase C-like - #120 / Putative auto-transporter adhesin, head GIN domain / Putative auto-transporter adhesin, head GIN domain / Pectate Lyase C-like / 3 Solenoid / Mainly Beta / Putative lipoprotein
Function and homology information
Biological speciesParabacteroides distasonis ATCC 8503 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.16 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of Putative lipid binding protein (YP_001304415.1) from Parabacteroides distasonis ATCC 8503 at 2.16 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionSep 18, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Feb 1, 2023Group: Database references / Derived calculations / Category: database_2 / 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_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)166,71547
Polymers162,9176
Non-polymers3,79941
Water31,1121727
1
A: Putative lipoprotein
B: Putative lipoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,84619
Polymers54,3062
Non-polymers1,54117
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5000 Å2
ΔGint-127 kcal/mol
Surface area20830 Å2
MethodPISA
2
C: Putative lipoprotein
D: Putative lipoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,43514
Polymers54,3062
Non-polymers1,12912
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4550 Å2
ΔGint-98 kcal/mol
Surface area20690 Å2
MethodPISA
3
E: Putative lipoprotein
F: Putative lipoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,43514
Polymers54,3062
Non-polymers1,12912
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4380 Å2
ΔGint-98 kcal/mol
Surface area20860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)201.880, 201.880, 202.840
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1116A24 - 269
2116B24 - 269
3116C24 - 269
4116D24 - 269
5116E24 - 269
6116F24 - 269

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Components

#1: Protein
Putative lipoprotein / Putative lipid binding protein


Mass: 27152.803 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Parabacteroides distasonis ATCC 8503 (bacteria)
Strain: ATCC 8503 / DSM 20701 / NCTC 11152 / Gene: BDI_3087, YP_001304415.1 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: A6LGH9
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1727 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE CONSTRUCT (RESIDUES 21-269) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG ...THE CONSTRUCT (RESIDUES 21-269) 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: 2

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)Description
16.3980.76THE STRUCTURE WAS PHASED BY MAD METHOD AT 2.31 A RESOLUTION AND REFINED AT 2.16 A RESOLUTION AGAINST A DATASET COLLECTED FROM A DIFFERENT CRYSTAL.
2
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2771vapor diffusion, sitting drop82.30M ammonium sulfate, 0.1M Bicine pH 8.0, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K
2772vapor diffusion, sitting drop8.292.50M ammonium sulfate, 0.1M Bicine pH 8.29, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21002
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSSRL BL11-110.97886
SYNCHROTRONSSRL BL11-120.97886,0.91837
Detector
TypeIDDetectorDateDetails
MARMOSAIC 325 mm CCD1CCDJul 8, 2009Flat mirror (vertical focusing)
MARMOSAIC 325 mm CCD2CCDJul 8, 2009Flat mirror (vertical focusing)
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Single crystal Si(111) bent monochromator (horizontal focusing)SINGLE WAVELENGTHMx-ray1
2Single crystal Si(111) bent monochromator (horizontal focusing)MADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.978861
20.918371
ReflectionResolution: 2.16→49.207 Å / Num. obs: 217900 / % possible obs: 96.7 % / Observed criterion σ(I): -3 / Redundancy: 3.76 % / Biso Wilson estimate: 37.203 Å2 / Rmerge(I) obs: 0.093 / Net I/σ(I): 8.91
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
2.16-2.310.7092.02149443395051,291.5
2.31-2.40.5362.672381190441,297.5
2.4-2.510.4283.274990197471,297.7
2.51-2.640.3354.173412193301,297.8
2.64-2.810.2325.676839202711,298
2.81-3.020.157.772642191991,298.1
3.02-3.330.09510.976577203131,298.3
3.33-3.810.05316.873860198471,298.1
3.81-4.780.0420.573129198361,298.3
4.78-49.2070.04521.475161208081,297.4

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0053refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3.006data extraction
XDSdata reduction
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.16→49.207 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.959 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 7.057 / SU ML: 0.079 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.122 / ESU R Free: 0.118
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. 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. 3. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 4. SULFATE (SO4), CHLORIDE (CL) AND GLYCEROL (GOL) MODELED ARE PRESENT IN CRYSTLLIZATION/CRYO CONDITIONS. 5. RAMACHANDRAN OUTLIERS (RESIDUES 186 AND 225) ARE SUPPORTED BY WELL DEFINED DENSITY.
RfactorNum. reflection% reflectionSelection details
Rfree0.21 10941 5 %RANDOM
Rwork0.187 ---
obs0.189 217881 97.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 91.85 Å2 / Biso mean: 30.091 Å2 / Biso min: 11.68 Å2
Baniso -1Baniso -2Baniso -3
1-0.19 Å20 Å20 Å2
2--0.19 Å20 Å2
3----0.38 Å2
Refinement stepCycle: LAST / Resolution: 2.16→49.207 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11166 0 221 1727 13114
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.02211677
X-RAY DIFFRACTIONr_bond_other_d0.0030.027929
X-RAY DIFFRACTIONr_angle_refined_deg1.5981.98815745
X-RAY DIFFRACTIONr_angle_other_deg0.911319549
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.75951526
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.99926490
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.592152109
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.7961544
X-RAY DIFFRACTIONr_chiral_restr0.0930.21754
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212992
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022104
X-RAY DIFFRACTIONr_mcbond_it0.6971.57405
X-RAY DIFFRACTIONr_mcbond_other0.1811.53092
X-RAY DIFFRACTIONr_mcangle_it1.455211949
X-RAY DIFFRACTIONr_scbond_it2.97434272
X-RAY DIFFRACTIONr_scangle_it4.94.53774
Refine LS restraints NCS

Ens-ID: 1 / Number: 3024 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1ALOOSE POSITIONAL0.175
2BLOOSE POSITIONAL0.175
3CLOOSE POSITIONAL0.155
4DLOOSE POSITIONAL0.225
5ELOOSE POSITIONAL0.195
6FLOOSE POSITIONAL0.245
1ALOOSE THERMAL1.0710
2BLOOSE THERMAL2.1910
3CLOOSE THERMAL1.7510
4DLOOSE THERMAL2.2210
5ELOOSE THERMAL2.6410
6FLOOSE THERMAL0.9410
LS refinement shellResolution: 2.157→2.213 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.333 808 -
Rwork0.304 14663 -
all-15471 -
obs--94.62 %
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)
10.8712-0.37760.57110.6487-0.36950.60810.07070.0874-0.0919-0.12440.0210.05120.15130.011-0.09170.0581-0.0071-0.02410.0726-0.02020.0193-26.518367.342617.3999
20.3905-0.19040.34310.5207-0.29820.6275-0.01490.01260.0070.03730.0395-0.0192-0.0031-0.0081-0.02450.0040.0012-0.00360.0323-0.00130.005-6.789184.271136.9064
30.9032-0.6094-0.38360.57410.33960.48780.05520.06780.0895-0.1129-0.0951-0.0546-0.0653-0.01660.040.04930.0310.01630.02930.01470.063523.993443.242727.2729
40.5014-0.5513-0.27180.95080.39720.4832-0.0943-0.12930.05160.05850.0625-0.09990.00360.08410.03180.0280.0296-0.00870.0583-0.00270.056643.505423.822144.2413
50.55210.17580.37290.51630.4790.82150.0545-0.00650.0197-0.0203-0.02870.0138-0.02670.0003-0.02580.0269-0.01090.01030.01-0.0070.008616.836894.021515.9752
60.5840.33610.29950.79380.44380.57370.02880.1211-0.0529-0.10230.0705-0.0839-0.01910.1672-0.09920.05130.00230.01890.0664-0.03380.025233.738474.3405-3.4919
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A23 - 269
2X-RAY DIFFRACTION2B23 - 269
3X-RAY DIFFRACTION3C23 - 269
4X-RAY DIFFRACTION4D24 - 269
5X-RAY DIFFRACTION5E23 - 269
6X-RAY DIFFRACTION6F23 - 269

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