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- PDB-3nqi: Crystal structure of a Putative lipoprotein (BF3042) from Bactero... -

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Basic information

Entry
Database: PDB / ID: 3nqi
TitleCrystal structure of a Putative lipoprotein (BF3042) from Bacteroides fragilis NCTC 9343 at 1.87 A resolution
ComponentsPutative lipoprotein
KeywordsLIPID BINDING PROTEIN / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


Immunoglobulin-like - #3220 / NigD-like N-terminal OB domain / NigD-like, N-terminal domain superfamily / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Prokaryotic membrane lipoprotein lipid attachment site profile. / Beta Barrel / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
ACETATE ION / : / DI(HYDROXYETHYL)ETHER / Lipoprotein / Lipoprotein
Similarity search - Component
Biological speciesBacteroides fragilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.87 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a Putative lipoprotein (BF3042) from Bacteroides fragilis NCTC 9343 at 1.87 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJun 29, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 18, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Jul 17, 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 / 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_alt_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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 / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_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
Revision 1.5Oct 30, 2024Group: Data collection / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
Item: _pdbx_entry_details.has_protein_modification / _struct_ncs_dom_lim.beg_auth_comp_id ..._pdbx_entry_details.has_protein_modification / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,78348
Polymers108,8124
Non-polymers3,97144
Water6,612367
1
A: Putative lipoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,18412
Polymers27,2031
Non-polymers98011
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Putative lipoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,75118
Polymers27,2031
Non-polymers1,54817
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Putative lipoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,99510
Polymers27,2031
Non-polymers7929
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Putative lipoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8538
Polymers27,2031
Non-polymers6507
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
A: Putative lipoprotein
B: Putative lipoprotein
hetero molecules

A: Putative lipoprotein
B: Putative lipoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,87060
Polymers108,8124
Non-polymers5,05756
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area14960 Å2
ΔGint-250 kcal/mol
Surface area44530 Å2
MethodPISA
6
C: Putative lipoprotein
D: Putative lipoprotein
hetero molecules

C: Putative lipoprotein
D: Putative lipoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,69636
Polymers108,8124
Non-polymers2,88432
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area11560 Å2
ΔGint-179 kcal/mol
Surface area44600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)157.490, 77.227, 97.406
Angle α, β, γ (deg.)90.000, 103.850, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLNGLNSERSER4AA31 - 12710 - 106
21GLNGLNSERSER4BB31 - 12710 - 106
31GLNGLNSERSER4CC31 - 12710 - 106
41GLNGLNSERSER4DD31 - 12710 - 106
12PHEPHETYRTYR6AA128 - 132107 - 111
22PHEPHETYRTYR6BB128 - 132107 - 111
32PHEPHETYRTYR6CC128 - 132107 - 111
42PHEPHETYRTYR6DD128 - 132107 - 111
13SERSERGLUGLU2AA133 - 267112 - 246
23SERSERGLUGLU2BB133 - 267112 - 246
33SERSERGLUGLU2CC133 - 267112 - 246
43SERSERGLUGLU2DD133 - 267112 - 246

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Putative lipoprotein


Mass: 27203.033 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides fragilis (bacteria) / Strain: ATCC 25285 / NCTC 9343 / Gene: BF3042 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q5LAY5, UniProt: A0A380YR22*PLUS

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Non-polymers , 5 types, 411 molecules

#2: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: Cd
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 367 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Sequence detailsTHE CONSTRUCT (RESIDUES 23-267) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG ...THE CONSTRUCT (RESIDUES 23-267) 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: 2.64 Å3/Da / Density % sol: 53.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.1
Details: 36.0000% polyethylene glycol 400, 0.1000M Cadmium Chloride, 0.1M sodium acetate pH 5.1, 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: 0.97939,0.91837,0.97922
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Nov 5, 2009 / Details: Flat collimating mirror, toroid focusing mirror
RadiationMonochromator: Double crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979391
20.918371
30.979221
ReflectionResolution: 1.87→47.287 Å / Num. obs: 93428 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 25.253 Å2 / Rmerge(I) obs: 0.071 / Net I/σ(I): 10.85
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.87-1.940.7532.135995970899.9
1.94-2.010.5252.931199836299.9
2.01-2.110.3813.8381151019499.9
2.11-2.220.2834.934555920999.9
2.22-2.360.2146.235066932299.9
2.36-2.540.1598.134636921299.9
2.54-2.790.11410.734406915199.8
2.79-3.190.07215.334847932999.7
3.19-4.020.04123.834896941799.1
4.02-47.2870.03530.434139943697.9

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0110refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3.006data extraction
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.87→47.287 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.948 / Occupancy max: 1 / Occupancy min: 0.2 / SU B: 6.084 / SU ML: 0.099 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.124
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 RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 4. WATERS WERE EXCLUDED FROM AUTOMATIC TLS ASSIGNMENT. 5. CADMIUM (CD) IONS, POLY ETHYLENE GLYCOL (PEG), CHLORIDE IONS (CL) AND ACETATE (ACT) MODELED WERE PRESENT IN CRYSTLLIZATION/CRYO CONDITIONS. 6. THE CADMIUM IONS ARE ASSIGNED BASED ON DENSITY AND ANOMALOUS DIFFERENCE FOURIERS. THE FLAGGED CLOSE CONTACTS ARE A RESULT OF MODELING ALTERNATE POSITIONS FOR SOME OF THE CD ATOMS BASED ON THE DENSITY, BUT IT WAS NOT POSSIBLE TO LOCATE THE REQUIRED LOW OCCUPANCY POSITIONS FOR SOME OF THE NEIGHBORING SIDE CHAINS.
RfactorNum. reflection% reflectionSelection details
Rfree0.22 4686 5 %RANDOM
Rwork0.191 ---
obs0.192 93425 99.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 109.56 Å2 / Biso mean: 39.988 Å2 / Biso min: 13.31 Å2
Baniso -1Baniso -2Baniso -3
1--1.17 Å20 Å2-0.47 Å2
2---1.79 Å20 Å2
3---2.73 Å2
Refinement stepCycle: LAST / Resolution: 1.87→47.287 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7102 0 122 367 7591
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0227565
X-RAY DIFFRACTIONr_bond_other_d0.0020.024972
X-RAY DIFFRACTIONr_angle_refined_deg1.4911.97510344
X-RAY DIFFRACTIONr_angle_other_deg0.925312311
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.28851000
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.54224.967302
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.863151294
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1631534
X-RAY DIFFRACTIONr_chiral_restr0.0890.21268
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0218328
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021414
X-RAY DIFFRACTIONr_mcbond_it1.5734749
X-RAY DIFFRACTIONr_mcbond_other0.57331892
X-RAY DIFFRACTIONr_mcangle_it2.65957805
X-RAY DIFFRACTIONr_scbond_it4.45782816
X-RAY DIFFRACTIONr_scangle_it6.641112494
Refine LS restraints NCS

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

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A784TIGHT POSITIONAL0.130.15
2B784TIGHT POSITIONAL0.140.15
3C784TIGHT POSITIONAL0.170.15
4D784TIGHT POSITIONAL0.140.15
1A1931MEDIUM POSITIONAL0.340.5
2B1931MEDIUM POSITIONAL0.360.5
3C1931MEDIUM POSITIONAL0.350.5
4D1931MEDIUM POSITIONAL0.470.5
1A37LOOSE POSITIONAL1.265
2B37LOOSE POSITIONAL1.585
3C37LOOSE POSITIONAL1.415
4D37LOOSE POSITIONAL1.65
1A784TIGHT THERMAL0.560.5
2B784TIGHT THERMAL0.550.5
3C784TIGHT THERMAL0.540.5
4D784TIGHT THERMAL0.380.5
1A1931MEDIUM THERMAL0.51
2B1931MEDIUM THERMAL0.491
3C1931MEDIUM THERMAL0.431
4D1931MEDIUM THERMAL0.351
1A37LOOSE THERMAL1.0210
2B37LOOSE THERMAL1.1110
3C37LOOSE THERMAL0.8110
4D37LOOSE THERMAL0.6710
LS refinement shellResolution: 1.87→1.918 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.327 361 -
Rwork0.3 6517 -
all-6878 -
obs--99.88 %
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)
19.1252.87453.57833.14762.53514.2697-0.0371-0.82430.74570.153-0.25430.0236-0.1459-0.3760.29140.1014-0.04070.00280.1858-0.07190.1255-11.793824.476817.971
21.6304-0.4034-0.13571.75820.12060.53680.01740.0031-0.12190.01170.0210.0976-0.01530.0006-0.03830.0118-0.01080.01140.04320.00620.0572-23.45486.74723.9836
38.8742-2.4431-1.79134.38560.7911.80310.05740.6711-0.482-0.2976-0.18850.17910.2105-0.18830.13110.10580.0384-0.00930.1692-0.04960.089-12.003123.6071-18.0791
42.43140.93780.3322.45740.17360.61490.02190.05890.18780.01120.0385-0.0285-0.01310.0658-0.06040.01430.0180.00280.0450.00330.141-23.497241.6188-3.9346
59.3726-3.2253-0.4774.9510.17792.44910.12370.7463-0.8997-0.3593-0.23040.02930.04170.10720.10660.39430.03720.01190.2458-0.0670.1084-14.1055-22.174326.5019
61.09120.18280.1312.11930.00290.8159-0.0409-0.01920.0895-0.1791-0.02960.4158-0.0025-0.10490.07040.30840.0339-0.06960.1352-0.01270.1151-30.8188-4.473232.9936
74.1861.52443.32862.84012.13345.7752-0.1386-0.57410.52280.0954-0.33560.351-0.3464-0.69930.47420.3773-0.00440.04620.3158-0.0840.2287-30.4401-21.403457.022
82.43-0.8530.38353.81610.19331.04260.0584-0.0935-0.11150.0413-0.03190.32890.0281-0.096-0.02650.3517-0.0132-0.03350.1446-0.01760.2215-34.7002-39.405439.9112
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A30 - 100
2X-RAY DIFFRACTION2A101 - 267
3X-RAY DIFFRACTION3B31 - 100
4X-RAY DIFFRACTION4B101 - 267
5X-RAY DIFFRACTION5C30 - 100
6X-RAY DIFFRACTION6C101 - 267
7X-RAY DIFFRACTION7D31 - 100
8X-RAY DIFFRACTION8D101 - 267

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