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- PDB-4ddd: Crystal structure of an immunogenic protein from ehrlichia chaffeensis -

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Basic information

Entry
Database: PDB / ID: 4ddd
TitleCrystal structure of an immunogenic protein from ehrlichia chaffeensis
ComponentsImmunogenic protein
KeywordsIMMUNE SYSTEM / SSGCID / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homologyTRAP transporter solute receptor, TAXI family / NMT1-like family / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta / Immunogenic protein
Function and homology information
Biological speciesEhrlichia chaffeensis (bacteria)
MethodX-RAY DIFFRACTION / SAD / Resolution: 1.9 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To be Published
Title: Crystal structure of an immunogenic protein from ehrlichia chaffeensis
Authors: Seattle Structural Genomics Center for Infectious Disease (SSGCID) / Abendroth, J. / Gardberg, A.S. / Staker, B.L.
History
DepositionJan 18, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 23, 2012Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Immunogenic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,3966
Polymers36,0821
Non-polymers3145
Water5,531307
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)62.710, 65.440, 90.970
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Immunogenic protein


Mass: 36082.160 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ehrlichia chaffeensis (bacteria) / Strain: ARKANSAS / Gene: ECH_0645 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q2GGH8
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 307 / Source method: isolated from a natural source / Formula: H2O

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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

CrystalDensity Matthews: 2.59 Å3/Da / Density % sol: 52.45 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: EBS SCREEN JCSG+ H6: 100MM BISTRIS PH 6.5, 17% PEG 10K, 100MM AMMONIUM ACETATE, EHCHA.00493.A.A2 PS01157 AT 18MG/ML; CRYSTAL FOR PHASING WAS SOAKED IN CRYSTALLIZATION BUFFER CONTAINING 1M ...Details: EBS SCREEN JCSG+ H6: 100MM BISTRIS PH 6.5, 17% PEG 10K, 100MM AMMONIUM ACETATE, EHCHA.00493.A.A2 PS01157 AT 18MG/ML; CRYSTAL FOR PHASING WAS SOAKED IN CRYSTALLIZATION BUFFER CONTAINING 1M IODIDE, PH 8.5., VAPOR DIFFUSION, SITTING DROP, temperature 290K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceTypeIDWavelengthWavelength (Å)
ROTATING ANODERIGAKU MICROMAX-007 HF11.54181.5418
ROTATING ANODERIGAKU MICROMAX-007 HF21.5418
Detector
TypeIDDetectorDateDetails
RIGAKU SATURN 9441CCDAug 12, 2011RIGAKU VARIMAX
RIGAKU SATURN 944+2CCDJan 9, 2012RIGAKU VARIMAX
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1RIGAKU VARIMAXSINGLE WAVELENGTHMx-ray1
2RIGAKU VARIMAXSINGLE WAVELENGTHMx-ray1
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 30172 / Num. obs: 29858 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.94 % / Biso Wilson estimate: 22.47 Å2 / Rmerge(I) obs: 0.061 / Rsym value: 0.061 / Net I/σ(I): 21.2
Reflection shellResolution: 1.9→1.95 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.309 / Mean I/σ(I) obs: 3.6 / Num. unique all: 2168 / Rsym value: 0.309 / % possible all: 91.3

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Processing

Software
NameVersionClassification
StructureStudiodata collection
PHASERphasing
REFMAC5.6.0117refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: SAD / Resolution: 1.9→45.49 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.942 / SU B: 4.519 / SU ML: 0.07 / Isotropic thermal model: isotropic, TLS / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.121 / ESU R Free: 0.113 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE
RfactorNum. reflection% reflectionSelection details
Rfree0.188 1515 5.1 %RANDOM
Rwork0.159 ---
all0.161 30172 --
obs0.161 29858 99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.57 Å2
Baniso -1Baniso -2Baniso -3
1--0.07 Å20 Å2-0 Å2
2--0.11 Å20 Å2
3----0.04 Å2
Refinement stepCycle: LAST / Resolution: 1.9→45.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2300 0 19 307 2626
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.022448
X-RAY DIFFRACTIONr_bond_other_d0.0010.021642
X-RAY DIFFRACTIONr_angle_refined_deg1.6851.9783329
X-RAY DIFFRACTIONr_angle_other_deg0.9623.0024056
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0375328
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.18825.05199
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.12215449
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1481510
X-RAY DIFFRACTIONr_chiral_restr0.1040.2390
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022715
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02459
LS refinement shellResolution: 1.9→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.261 92 -
Rwork0.217 1762 -
obs-1980 90.53 %
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)
10.6224-0.1866-0.09770.7775-0.29310.6092-0.0208-0.05950.00710.03310.0269-0.0238-0.0010.0134-0.00610.02610.00510.00630.01180.00140.01447.40448.69413.314
20.80630.2924-0.08551.01540.37440.922-0.0072-0.01520.0414-0.0405-0.0222-0.0029-0.0379-0.00440.02930.04290.00140.0080.00330.0030.0106-3.2271.4457.839
31.5356-0.6772-0.01740.9471-0.17850.4750.01740.0981-0.1152-0.0865-0.02360.05490.0116-0.00620.00620.027-0.0061-0.00520.0215-0.00970.01644.22843.5291.351
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A26 - 122
2X-RAY DIFFRACTION2A123 - 259
3X-RAY DIFFRACTION3A260 - 325

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