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- PDB-4noh: 1.5 Angstrom Crystal Structure of Putative Lipoprotein from Bacil... -

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Basic information

Entry
Database: PDB / ID: 4noh
Title1.5 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 / homology
Function and homology information


Barwin-like endoglucanases - #60 / Alpha-Beta Plaits - #3060 / Putative lipoprotein, bacteria / Uncharacterised lipoprotein family / Barwin-like endoglucanases / Alpha-Beta Plaits / Beta Barrel / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Putative lipoprotein / Putative lipoprotein
Similarity search - Component
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.502 Å
AuthorsMinasov, G. / Shuvalova, L. / Halavaty, A. / Winsor, J. / Dubrovska, I. / Shatsman, S. / Kwon, K. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: TO BE PUBLISHED
Title: 1.5 Angstrom Crystal Structure of Putative Lipoprotein from Bacillus anthracis.
Authors: Minasov, G. / Shuvalova, L. / Halavaty, A. / Winsor, J. / Dubrovska, I. / Shatsman, S. / Kwon, K. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionNov 19, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 4, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,6663
Polymers38,6302
Non-polymers351
Water5,206289
1
A: Lipoprotein, putative


Theoretical massNumber of molelcules
Total (without water)19,3151
Polymers19,3151
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Lipoprotein, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,3502
Polymers19,3151
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)40.927, 74.267, 47.382
Angle α, β, γ (deg.)90.00, 91.90, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Lipoprotein, putative / Putative lipoprotein


Mass: 19315.027 Da / Num. of mol.: 2 / Fragment: putative lipoprotein
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Strain: Ames / Gene: BA_5634, BAS5236, GBAA_5634 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Magic / References: UniProt: Q81JR6, UniProt: A0A6L8PXC8*PLUS
#2: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 289 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE CRYSTAL GREW AFTER A YEAR AND IT IS BELIEVED THAT AN ADDITIONAL N-TERMINAL SEQUENCE (MSE) ...THE CRYSTAL GREW AFTER A YEAR AND IT IS BELIEVED THAT AN ADDITIONAL N-TERMINAL SEQUENCE (MSE)HHHHHHSSGVDLGTENLYFQ WAS CLEAVED IN THE PROCESS

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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: 1.86 Å3/Da / Density % sol: 33.98 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 9
Details: Protein: 7.5 mG/mL, 0.5 M Sodium chloride, 0.01 M Tris-HCL buffer pH 8.3; Screen: PACT (C3), 0.1M MMT buffer pH 9.0, 25% (v/v) PEG 1500, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97911 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 14, 2013 / Details: Mirrors
RadiationMonochromator: Si {1,1,1} / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97911 Å / Relative weight: 1
ReflectionResolution: 1.5→30 Å / Num. all: 44692 / Num. obs: 44692 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 18.6 Å2 / Rmerge(I) obs: 0.086 / Rsym value: 0.086 / Net I/σ(I): 19.4
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 2.4 / Num. unique all: 2214 / Rsym value: 0.57 / % possible all: 98.7

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Processing

Software
NameVersionClassification
Blu-IceMaxdata collection
SHELXSphasing
REFMAC5.8.0046refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.502→29.22 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.959 / SU B: 3.043 / SU ML: 0.056
Isotropic thermal model: Thermal Factors Individually Isotropically Refined
Cross valid method: THROUGHOUT / ESU R: 0.08 / ESU R Free: 0.082 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19709 2254 5 %RANDOM
Rwork0.16098 ---
all0.16283 42391 --
obs0.16283 42391 98.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.334 Å2
Baniso -1Baniso -2Baniso -3
1--0.58 Å20 Å20.08 Å2
2--0.61 Å20 Å2
3----0.04 Å2
Refinement stepCycle: LAST / Resolution: 1.502→29.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2618 0 1 289 2908
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0192850
X-RAY DIFFRACTIONr_bond_other_d0.0010.022864
X-RAY DIFFRACTIONr_angle_refined_deg1.5232.0153834
X-RAY DIFFRACTIONr_angle_other_deg0.69536700
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.5925371
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.17127.414116
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.39915561
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.146154
X-RAY DIFFRACTIONr_chiral_restr0.0920.2424
X-RAY DIFFRACTIONr_gen_planes_refined0.0180.023205
X-RAY DIFFRACTIONr_gen_planes_other0.0170.02515
X-RAY DIFFRACTIONr_mcbond_it1.1821.2981439
X-RAY DIFFRACTIONr_mcbond_other1.1781.2971438
X-RAY DIFFRACTIONr_mcangle_it1.8581.9421825
X-RAY DIFFRACTIONr_mcangle_other1.8591.9431826
X-RAY DIFFRACTIONr_scbond_it2.2061.6121411
X-RAY DIFFRACTIONr_scbond_other2.2041.6121411
X-RAY DIFFRACTIONr_scangle_other3.4212.2932009
X-RAY DIFFRACTIONr_long_range_B_refined6.07211.9273291
X-RAY DIFFRACTIONr_long_range_B_other5.99611.3643178
LS refinement shellResolution: 1.502→1.541 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.273 143 -
Rwork0.234 2932 -
obs-2932 92.15 %
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)
10.6405-0.15310.4772.3411-0.53211.3495-0.0432-0.0597-0.02740.018-0.0144-0.17110.0628-0.09030.05750.03780.00290.0030.0188-0.00550.023215.432813.808224.275
21.6516-0.4415-1.48543.0930.67212.69730.0845-0.06130.18450.03070.0457-0.0445-0.0397-0.0624-0.13020.01350.00130.00310.0196-0.0150.036912.480330.597115.5736
31.9416-0.4019-0.70571.45290.18072.48930.1130.16470.0719-0.01740.14540.09470.0657-0.3911-0.25840.0194-0.0025-0.00890.0920.05320.03782.335229.807511.8601
41.31630.0851-0.99221.5631-0.87722.4870.09880.07430.14090.03580.1219-0.0322-0.1934-0.1268-0.22070.01990.01190.01780.02590.00350.03228.254632.695414.325
52.03210.94220.30442.6034-0.88181.8168-0.0123-0.1602-0.02750.1224-0.02370.0179-0.0059-0.14090.0360.04150.00960.0120.0628-0.01780.014310.12216.072727.132
63.0625-0.3539-0.35351.39960.08921.5140.09810.19010.0992-0.1131-0.04180.0976-0.146-0.0993-0.05640.04360.01240.00780.02180.01610.034317.414843.595333.6012
72.12950.328-0.01732.08650.36832.00970.071-0.16850.09250.1018-0.04280.06170.05320.0417-0.02820.0164-0.01180.00620.0269-0.00530.008430.929734.050842.5402
81.6868-0.2798-0.47411.7670.02543.5805-0.0059-0.1815-0.2336-0.06540.0483-0.14980.50260.2155-0.04240.1060.0262-0.01320.09230.02240.057936.663123.086443.1027
92.59030.0874-0.79411.11430.48711.7399-0.0133-0.0282-0.1509-0.0141-0.00890.03650.03750.01030.02210.0175-0.005-0.00620.0120.01120.020429.430129.00938.8234
103.4144-0.7903-0.39341.05910.45343.16850.0922-0.0489-0.00650.0903-0.03760.0507-0.2763-0.2099-0.05460.07430.01450.04060.02690.00770.034414.811942.788540.2785
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 57
2X-RAY DIFFRACTION2A58 - 81
3X-RAY DIFFRACTION3A82 - 126
4X-RAY DIFFRACTION4A127 - 159
5X-RAY DIFFRACTION5A160 - 196
6X-RAY DIFFRACTION6B0 - 59
7X-RAY DIFFRACTION7B60 - 104
8X-RAY DIFFRACTION8B105 - 130
9X-RAY DIFFRACTION9B131 - 161
10X-RAY DIFFRACTION10B162 - 196

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