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- PDB-2grv: Crystal Structure of LpqW -

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Basic information

Entry
Database: PDB / ID: 2grv
TitleCrystal Structure of LpqW
ComponentsLpqW
KeywordsBIOSYNTHETIC PROTEIN / substrate-binding protein scaffold
Function / homology
Function and homology information


glycolipid biosynthetic process / phosphatidylinositol metabolic process / phospholipid biosynthetic process
Similarity search - Function
Dipeptide-binding Protein; domain 1 / Dipeptide-binding Protein; Domain 1 / Dipeptide-binding Protein; domain 3 / Dipeptide-binding Protein; Domain 3 / Solute-binding protein family 5 domain / Solute-binding protein family 5 / Bacterial extracellular solute-binding proteins, family 5 Middle / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / Roll ...Dipeptide-binding Protein; domain 1 / Dipeptide-binding Protein; Domain 1 / Dipeptide-binding Protein; domain 3 / Dipeptide-binding Protein; Domain 3 / Solute-binding protein family 5 domain / Solute-binding protein family 5 / Bacterial extracellular solute-binding proteins, family 5 Middle / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / Roll / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Probable monoacyl phosphatidylinositol tetramannoside-binding protein LpqW / :
Similarity search - Component
Biological speciesMycobacterium smegmatis str. MC2 155 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.4 Å
AuthorsMarland, Z. / Rossjohn, J.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: Hijacking of a Substrate-binding Protein Scaffold for use in Mycobacterial Cell Wall Biosynthesis
Authors: Marland, Z. / Beddoe, T. / Zaker-Tabrizi, L. / Lucet, I.S. / Brammananth, R. / Whisstock, J.C. / Wilce, M.C. / Coppel, R.L. / Crellin, P.K. / Rossjohn, J.
History
DepositionApr 25, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 18, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.4Oct 23, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_unobs_or_zero_occ_atoms / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: LpqW
B: LpqW
C: LpqW


Theoretical massNumber of molelcules
Total (without water)195,9123
Polymers195,9123
Non-polymers00
Water9,656536
1
A: LpqW


Theoretical massNumber of molelcules
Total (without water)65,3041
Polymers65,3041
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: LpqW


Theoretical massNumber of molelcules
Total (without water)65,3041
Polymers65,3041
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: LpqW


Theoretical massNumber of molelcules
Total (without water)65,3041
Polymers65,3041
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)188.572, 312.035, 104.145
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number21
Space group name H-MC222
Components on special symmetry positions
IDModelComponents
11A-749-

HOH

21B-667-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
12A
22C
13A

NCS domain segments:

Component-ID: 1 / Refine code: 3

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALAALAVALVALAA25 - 36346 - 384
12ARGARGLEULEUAA379 - 466400 - 487
22ARGARGLEULEUCC379 - 466400 - 487
13GLNGLNTHRTHRAA516 - 599537 - 620

NCS ensembles :
ID
1
2
3
DetailsThe biological assembly is a monomer

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Components

#1: Protein LpqW


Mass: 65304.008 Da / Num. of mol.: 3 / Fragment: Ectodomain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium smegmatis str. MC2 155 (bacteria)
Species: Mycobacterium smegmatis / Strain: MC2155 / Gene: lpqW / Plasmid: pET28b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q1TT16, UniProt: A0R2I8*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 536 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.91 Å3/Da / Density % sol: 68.51 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 20-24% PEG 4000, 8-16% 2-propanol, 0.1M sodium citrate, 10mM DTT, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 30, 2004
RadiationMonochromator: Bent Ge(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.4→158.11 Å / Num. obs: 115857 / % possible obs: 97.1 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.081 / Net I/σ(I): 17.9
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 3 % / Rmerge(I) obs: 0.577 / Mean I/σ(I) obs: 2.1 / Num. unique all: 10998 / % possible all: 93

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
ADSCdata collection
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
DMphasing
RefinementMethod to determine structure: MIR / Resolution: 2.4→100 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.925 / SU B: 13.523 / SU ML: 0.165 / Cross valid method: THROUGHOUT / ESU R: 0.228 / ESU R Free: 0.198 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.247 3473 3 %RANDOM
Rwork0.2159 ---
obs0.21684 112319 96.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 59.308 Å2
Baniso -1Baniso -2Baniso -3
1--2.83 Å20 Å20 Å2
2--3.43 Å20 Å2
3----0.61 Å2
Refinement stepCycle: LAST / Resolution: 2.4→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11479 0 0 536 12015
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.02211668
X-RAY DIFFRACTIONr_angle_refined_deg1.0371.97116025
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.99951527
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.73824.355473
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.212151708
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7281587
X-RAY DIFFRACTIONr_chiral_restr0.0640.21897
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.029009
X-RAY DIFFRACTIONr_nbd_refined0.1820.25311
X-RAY DIFFRACTIONr_nbtor_refined0.2980.28015
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1220.2673
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2010.260
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.190.213
X-RAY DIFFRACTIONr_mcbond_it0.73637885
X-RAY DIFFRACTIONr_mcangle_it1.354512451
X-RAY DIFFRACTIONr_scbond_it2.09274287
X-RAY DIFFRACTIONr_scangle_it3.246103574
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION

Ens-IDNumberTypeRms dev position (Å)Weight position
2352tight positional0.040.05
3336tight positional0.030.05
2268loose positional0.45
3269loose positional0.275
2352tight thermal0.10.5
3336tight thermal0.050.5
2268loose thermal1.710
3269loose thermal1.4510
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.374 226 -
Rwork0.32 7362 -
obs--86.38 %
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)
11.97530.24790.04371.3660.22260.8290.104-0.3887-0.456-0.0252-0.1179-0.14420.10270.13690.014-0.1891-0.0298-0.0204-0.12020.2144-0.045535.84151.1868.72
21.83760.12160.03681.78760.18280.60140.0301-0.43220.0543-0.0939-0.0807-0.18-0.09130.08770.0506-0.2125-0.0934-0.0404-0.10150.0471-0.196237.21671.88168.38
32.06070.08280.34491.8120.66651.74150.0932-0.6066-0.4030.1429-0.0437-0.03520.2119-0.028-0.0494-0.1872-0.1061-0.043-0.02280.2079-0.135228.11554.52974.811
42.09660.38210.7261.3640.52832.05920.0838-0.5389-0.04750.3794-0.39540.28050.1435-0.64040.31170.1461-0.09960.1848-0.074-0.10380.0893-19.6-16.19816.341
52.00030.88260.60491.74230.782.9132-0.1192-0.14640.1065-0.0496-0.33020.467-0.0606-0.74130.44940.0009-0.02460.0554-0.0646-0.23060.1989-26.092-17.766-3.41
63.48431.08990.78631.85471.06632.55890.2714-0.4569-0.52710.5472-0.43430.12490.6041-0.74940.16290.2914-0.25830.2116-0.119-0.03530.1641-21.538-26.35314.344
72.63140.23671.09291.07230.36192.2779-0.06250.7301-0.1363-0.1382-0.0156-0.1182-0.24880.38110.0781-0.137-0.00920.0211-0.0026-0.0365-0.26216.01568.0126.262
83.1842-1.04351.37872.2227-1.1533.2730.26140.479-0.9332-0.26240.0096-0.06370.6120.0345-0.271-0.05640.0243-0.0561-0.1523-0.2390.007710.29748.2729.519
94.01661.0471.48031.10670.352.4586-0.13620.41050.0493-0.0852-0.04120.0356-0.37160.02720.1774-0.13870.0619-0.0081-0.1552-0.0673-0.29496.4468.23130.017
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA25 - 27846 - 299
2X-RAY DIFFRACTION1AA279 - 366300 - 387
3X-RAY DIFFRACTION2AA379 - 468400 - 489
4X-RAY DIFFRACTION3AA516 - 566537 - 587
5X-RAY DIFFRACTION3AA567 - 599588 - 620
6X-RAY DIFFRACTION4BB25 - 27846 - 299
7X-RAY DIFFRACTION4BB279 - 362300 - 383
8X-RAY DIFFRACTION5BB379 - 466400 - 487
9X-RAY DIFFRACTION6BB517 - 566538 - 587
10X-RAY DIFFRACTION6BB567 - 599588 - 620
11X-RAY DIFFRACTION7CC25 - 27846 - 299
12X-RAY DIFFRACTION7CC279 - 363300 - 384
13X-RAY DIFFRACTION8CC379 - 466400 - 487
14X-RAY DIFFRACTION9CC516 - 566537 - 587
15X-RAY DIFFRACTION9CC567 - 599588 - 620

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