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- PDB-4o4a: 2.75 Angstrom Crystal Structure of Putative Lipoprotein from Baci... -

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Entry
Database: PDB / ID: 4o4a
Title2.75 Angstrom Crystal Structure of Putative Lipoprotein from Bacillus anthracis.
ComponentsLipoprotein, putative
KeywordsLIPID BINDING PROTEIN / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Center for Structural Genomics of Infectious Diseases / CSGID / putative lipoprotein
Function / homologyPutative lipoprotein BA_2398-like / : / Family of unknown function (DUF6843) / Prokaryotic membrane lipoprotein lipid attachment site profile. / DI(HYDROXYETHYL)ETHER / Lipoprotein / Lipoprotein
Function and homology information
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.75 Å
AuthorsMinasov, G. / Halavaty, A. / Shuvalova, L. / Winsor, J. / Dubrovska, I. / Shatsman, S. / Kwon, K. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: TO BE PUBLISHED
Title: 2.75 Angstrom Crystal Structure of Putative Lipoprotein from Bacillus anthracis.
Authors: Minasov, G. / Halavaty, A. / Shuvalova, L. / Winsor, J. / Dubrovska, I. / Shatsman, S. / Kwon, K. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionDec 18, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 1, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_conn / struct_ncs_dom_lim / 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_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 / _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: Lipoprotein, putative
B: Lipoprotein, putative
C: Lipoprotein, putative
D: Lipoprotein, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,46110
Polymers78,6884
Non-polymers7736
Water1,63991
1
A: Lipoprotein, putative
D: Lipoprotein, putative
hetero molecules

B: Lipoprotein, putative
C: Lipoprotein, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,46110
Polymers78,6884
Non-polymers7736
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-y+1/2,x+1/2,z+1/21
Buried area4020 Å2
ΔGint-60 kcal/mol
Surface area32950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.556, 122.556, 107.354
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / Refine code: _

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASNASNAA33 - 17426 - 167
21ASNASNBB33 - 17426 - 167
12LYSLYSAA33 - 17526 - 168
22LYSLYSCC33 - 17526 - 168
13ASNASNAA33 - 17426 - 167
23ASNASNDD33 - 17426 - 167
14ASNASNBB33 - 17426 - 167
24ASNASNCC33 - 17426 - 167
15VALVALBB33 - 17626 - 169
25VALVALDD33 - 17626 - 169
16ASNASNCC33 - 17426 - 167
26ASNASNDD33 - 17426 - 167

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Lipoprotein, putative / Putative lipoprotein


Mass: 19671.953 Da / Num. of mol.: 4 / Fragment: Putative Lipoprotein
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Strain: Ames / Gene: BA_2398, BAS2234, GBAA_2398 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): KRX / References: UniProt: Q81QM6, UniProt: A0A6L8PAP6*PLUS
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 91 / 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.56 Å3/Da / Density % sol: 51.98 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Protein: 7.2 mG/mL, 0.5 M Sodium chloride, 0.01 M Tris-HCL buffer pH 8.3; Screen: Classics II (F8), 0.2M Ammonium sulfate, 0.1M HEPES pH 7.5, 25% (w/v) PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 21, 2013 / Details: Beryllium lenses
RadiationMonochromator: Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.75→30 Å / Num. all: 21759 / Num. obs: 21759 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 9.6 % / Biso Wilson estimate: 70.9 Å2 / Rmerge(I) obs: 0.092 / Rsym value: 0.092 / Net I/σ(I): 27.5
Reflection shellResolution: 2.75→2.8 Å / Redundancy: 9.9 % / Rmerge(I) obs: 0.543 / Mean I/σ(I) obs: 4.7 / Num. unique all: 1055 / Rsym value: 0.543 / % possible all: 100

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Processing

Software
NameVersionClassification
Blu-IceMaxdata collection
SHELXSphasing
REFMAC5.7.0032refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.75→29.96 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.9 / SU B: 27.445 / SU ML: 0.265
Isotropic thermal model: Thermal Factors Individually Isotropically Refined
Cross valid method: THROUGHOUT / ESU R: 1.047 / ESU R Free: 0.341 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25278 1107 5.1 %RANDOM
Rwork0.20918 ---
all0.21137 20596 --
obs0.21137 20596 99.36 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 65.046 Å2
Baniso -1Baniso -2Baniso -3
1-0.32 Å20 Å20 Å2
2--0.32 Å2-0 Å2
3----0.65 Å2
Refinement stepCycle: LAST / Resolution: 2.75→29.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4628 0 46 91 4765
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0194770
X-RAY DIFFRACTIONr_bond_other_d0.0050.024360
X-RAY DIFFRACTIONr_angle_refined_deg1.5581.9686449
X-RAY DIFFRACTIONr_angle_other_deg1.128310089
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.7475576
X-RAY DIFFRACTIONr_dihedral_angle_2_deg24.49825.102245
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.43715784
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9241528
X-RAY DIFFRACTIONr_chiral_restr0.0840.2705
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0215406
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021070
X-RAY DIFFRACTIONr_mcbond_it2.7553.1652313
X-RAY DIFFRACTIONr_mcbond_other2.7553.1642312
X-RAY DIFFRACTIONr_mcangle_it4.4394.742886
X-RAY DIFFRACTIONr_mcangle_other4.4384.7412887
X-RAY DIFFRACTIONr_scbond_it3.8843.7282457
X-RAY DIFFRACTIONr_scbond_other3.7843.6952441
X-RAY DIFFRACTIONr_scangle_other5.8815.3253540
X-RAY DIFFRACTIONr_long_range_B_refined8.33725.8515192
X-RAY DIFFRACTIONr_long_range_B_other8.33425.8295182
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A70170.17
12B70170.17
21A72700.16
22C72700.16
31A71540.16
32D71540.16
41B74460.14
42C74460.14
51B74700.13
52D74700.13
61C73890.14
62D73890.14
LS refinement shellResolution: 2.75→2.821 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.306 85 -
Rwork0.302 1417 -
obs-1417 96.34 %
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)
13.0369-1.1783-0.36363.54030.048311.64310.4094-0.1301-0.0172-0.35470.21290.00111.48050.2025-0.62230.4351-0.0041-0.20050.0325-0.04920.221427.221974.149.2289
22.71668.19460.430139.665912.31948.3439-0.3195-0.173-0.7524-0.66731.3135-3.62050.3331.6056-0.99390.71780.27820.03170.82670.04080.66837.803471.787147.7777
38.57440.88453.70964.51840.90052.24270.6856-0.1245-0.6018-0.126-0.04150.00550.2624-0.4512-0.6440.14980.0197-0.08040.37870.15960.380225.293884.743951.7341
40.219-0.11470.23228.483-0.46932.15540.1683-0.07580.02820.18860.1041-0.07891.0033-0.1167-0.27240.618-0.0515-0.19530.1144-0.00450.303328.969369.265561.7309
51.5448-0.27480.29453.6913-0.57325.20560.1038-0.140.21230.4622-0.00540.2537-0.49390.0435-0.09830.2291-0.06840.02850.052-0.00390.189528.760245.32436.4149
61.5098-1.0051-0.45915.10140.95174.77510.21330.0837-0.0724-0.2571-0.0129-0.0802-0.3437-0.1303-0.20050.1878-0.0395-0.07490.07260.06390.142830.14143.548126.7819
73.8685-4.9693-4.740412.885711.989721.53230.2211-0.1861-0.0605-0.7323-0.30770.051-1.6755-0.03280.08660.5344-0.02020.00280.06440.02750.180130.073456.130120.8021
826.62726.99823.98375.07595.23426.01730.05870.728-0.76480.15930.4418-0.5580.2090.3885-0.50050.53630.0558-0.03710.18930.04730.394428.834369.21835.7063
91.9862-1.0453-0.08269.9605-2.911610.9180.00240.0582-0.30820.45340.6510.0309-0.4817-0.5019-0.65340.35570.23740.0640.23510.10630.289730.00370.27826.0146
102.6948-1.19841.975110.6508-1.75269.8077-0.1393-0.1210.03680.58470.2926-0.08440.02410.1801-0.15330.37310.22390.0940.14830.07780.117332.622267.01789.3368
112.4335-4.9662-0.774711.2746-0.51474.95190.0374-0.06220.3243-0.11630.2804-0.43910.10.0924-0.31780.31570.11880.08420.23580.07250.271333.93872.4205-1.9216
125.8097-2.5506-1.69294.16362.46149.782-0.0184-0.3305-0.7797-0.06280.17820.5666-0.1608-0.9422-0.15970.37740.18650.04420.26470.14930.299924.430175.4213-5.9927
133.99080.71270.12882.42010.28144.22950.1882-0.15430.17920.0577-0.25710.2821-0.0218-0.86930.06890.05420.067-0.03590.3949-0.13190.13568.812291.537122.1504
1432.1365-22.6358-13.419623.390913.13569.55260.5723-0.2746-1.0344-0.284-0.31130.6225-0.10790.278-0.2610.305-0.0103-0.10130.2562-0.0780.248223.979591.051428.6382
153.4659-1.8118-2.28384.54073.68897.27280.1293-0.23820.3140.5211-0.1913-0.15970.4933-0.38290.0620.2413-0.0286-0.05620.2518-0.08540.113615.391490.217934.7938
1638.2883-10.25145.540728.0863-6.291814.90860.70980.70620.7048-0.81-1.1324-0.06881.43351.09750.42260.55520.2330.00550.2602-0.04020.276427.240673.583221.4073
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A33 - 80
2X-RAY DIFFRACTION2A81 - 90
3X-RAY DIFFRACTION3A91 - 113
4X-RAY DIFFRACTION4A114 - 175
5X-RAY DIFFRACTION5B0 - 98
6X-RAY DIFFRACTION6B99 - 149
7X-RAY DIFFRACTION7B150 - 171
8X-RAY DIFFRACTION8B172 - 177
9X-RAY DIFFRACTION9C33 - 61
10X-RAY DIFFRACTION10C62 - 106
11X-RAY DIFFRACTION11C107 - 143
12X-RAY DIFFRACTION12C144 - 175
13X-RAY DIFFRACTION13D33 - 112
14X-RAY DIFFRACTION14D113 - 122
15X-RAY DIFFRACTION15D123 - 171
16X-RAY DIFFRACTION16D172 - 177

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