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- PDB-3l3b: Crystal structure of isoprenoid biosynthesis protein with amidotr... -

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Basic information

Entry
Database: PDB / ID: 3l3b
TitleCrystal structure of isoprenoid biosynthesis protein with amidotransferase-like domain from Ehrlichia Chaffeensis at 1.90A resolution
ComponentsEs1 family protein
KeywordsBIOSYNTHETIC PROTEIN / SSGCID / NIH / NIAID / SBRI / UW / EMERALD BIOSTRUCTURES / ALS COLLABORATIVE CRYSTALLOGRAPHY / EHRLICHIA CHAFFEENSIS / ISOPRENOID BIOSYNTHESIS / AMIDOTRANSFERASE-LIKE DOMAIN / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homologyDJ-1/PfpI / DJ-1/PfpI family / Class I glutamine amidotransferase (GATase) domain / Class I glutamine amidotransferase-like / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / Es1 family protein
Function and homology information
Biological speciesEhrlichia chaffeensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To be Published
Title: Crystal structure of isoprenoid biosynthesis protein with amidotransferase-like domain from Ehrlichia Chaffeensis at 1.90A resolution
Authors: Seattle Structural Genomics Center for Infectious Disease (SSGCID) / Abendroth, J. / Sankaran, B. / Edwards, T.E. / Staker, B.
History
DepositionDec 16, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 19, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.3Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_special_symmetry / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Es1 family protein
B: Es1 family protein


Theoretical massNumber of molelcules
Total (without water)53,8382
Polymers53,8382
Non-polymers00
Water2,900161
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3440 Å2
ΔGint-9 kcal/mol
Surface area15460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.210, 69.220, 242.050
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-299-

HOH

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Components

#1: Protein Es1 family protein


Mass: 26918.943 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ehrlichia chaffeensis (bacteria) / Strain: ARKANSAS / Gene: ECH_0012 / Plasmid: AVA0421 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q2GI86
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 161 / 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: 1

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Sample preparation

CrystalDensity Matthews: 1.88 Å3/Da / Density % sol: 34.41 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 0
Details: EBS JCSG+ SCREEN G10: 150mM Postassium bromice, 30% PEG 2000 MME; EHCHA.01061.A AT 20MG/ML, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 5, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 32591 / Num. obs: 32534 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 8.3 % / Biso Wilson estimate: 39.45 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 20.59
Reflection shellResolution: 1.9→1.95 Å / Redundancy: 7.7 % / Rmerge(I) obs: 0.465 / Mean I/σ(I) obs: 4.4 / Num. unique all: 2347 / % possible all: 99.8

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Processing

Software
NameVersionClassification
BOSdata collection
PHASERphasing
REFMAC5.5.0104refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb deposition 1vhq modified with CCP4 program CHAINSAW

1vhq


Resolution: 1.9→39.56 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.952 / SU B: 9.237 / SU ML: 0.117 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: isotropic, tls / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.161 / ESU R Free: 0.141 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE
RfactorNum. reflection% reflectionSelection details
Rfree0.221 1613 5 %RANDOM
Rwork0.191 ---
all0.192 32591 --
obs0.192 32472 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 10.96 Å2
Baniso -1Baniso -2Baniso -3
1--0.44 Å2-0 Å20 Å2
2--0.39 Å2-0 Å2
3---0.05 Å2
Refinement stepCycle: LAST / Resolution: 1.9→39.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3172 0 0 161 3333
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0223219
X-RAY DIFFRACTIONr_bond_other_d0.0010.022078
X-RAY DIFFRACTIONr_angle_refined_deg1.5281.9584362
X-RAY DIFFRACTIONr_angle_other_deg0.97435093
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2965418
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.96924.667135
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.66715527
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.221516
X-RAY DIFFRACTIONr_chiral_restr0.0950.2515
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023622
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02630
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8631.52095
X-RAY DIFFRACTIONr_mcbond_other0.2561.5859
X-RAY DIFFRACTIONr_mcangle_it1.48123354
X-RAY DIFFRACTIONr_scbond_it2.53831124
X-RAY DIFFRACTIONr_scangle_it3.8954.51008
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.383 127 -
Rwork0.294 2208 -
obs--99.83 %
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)
12.1516-0.27882.22441.101-0.39465.60730.15830.3785-0.0657-0.0134-0.04390.074-0.1249-0.2472-0.11440.12020.0208-0.01020.38680.04440.04311.92516.33677.336
21.1352-0.53120.97131.7275-1.95195.1249-0.0545-0.0515-0.0850.31530.13670.0217-0.0727-0.0975-0.08220.2669-0.045-0.01490.18320.0450.057320.24310.169103.379
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 218
2X-RAY DIFFRACTION1A222 - 301
3X-RAY DIFFRACTION2B2 - 219
4X-RAY DIFFRACTION2B222 - 302

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