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- PDB-5dn8: 1.76 Angstrom Crystal Structure of GTP-binding Protein Der from C... -

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Basic information

Entry
Database: PDB / ID: 5dn8
Title1.76 Angstrom Crystal Structure of GTP-binding Protein Der from Coxiella burnetii in Complex with GDP.
ComponentsGTPase Der
KeywordsGTP-binding protein / GDP / Complex / Structural genomics / CSGID / Center for Structural Genomics of Infectious Diseases
Function / homology
Function and homology information


ribosome biogenesis / ribosome binding / GTP binding
Similarity search - Function
EngA-type guanine nucleotide-binding (G) domain / EngA-type guanine nucleotide-binding (G) domain profile. / GTP-binding protein EngA / GTPase Der, C-terminal KH-domain-like / KH-domain-like of EngA bacterial GTPase enzymes, C-terminal / K homology (KH) domain / 50S ribosome-binding GTPase / GTP binding domain / GMP Synthetase; Chain A, domain 3 / Small GTP-binding protein domain ...EngA-type guanine nucleotide-binding (G) domain / EngA-type guanine nucleotide-binding (G) domain profile. / GTP-binding protein EngA / GTPase Der, C-terminal KH-domain-like / KH-domain-like of EngA bacterial GTPase enzymes, C-terminal / K homology (KH) domain / 50S ribosome-binding GTPase / GTP binding domain / GMP Synthetase; Chain A, domain 3 / Small GTP-binding protein domain / K homology domain-like, alpha/beta / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / GTPase Der
Similarity search - Component
Biological speciesCoxiella burnetii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 Å
AuthorsMinasov, G. / Shuvalova, L. / Han, A. / Kim, H.-Y. / Grimshaw, S. / Kwon, K. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To Be Published
Title: 1.76 Angstrom Crystal Structure of GTP-binding Protein Der from Coxiella burnetii in Complex with GDP.
Authors: Minasov, G. / Shuvalova, L. / Han, A. / Kim, H.-Y. / Grimshaw, S. / Kwon, K. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionSep 9, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 14, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 27, 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_prerelease_seq / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GTPase Der
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,9373
Polymers50,0501
Non-polymers8862
Water5,423301
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1250 Å2
ΔGint-9 kcal/mol
Surface area19830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.275, 98.443, 107.968
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 GTPase Der / GTP-binding protein EngA


Mass: 50050.398 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Coxiella burnetii (strain RSA 493 / Nine Mile phase I) (bacteria)
Strain: RSA 493 / Nine Mile phase I / Gene: der, engA, CBU_1245 / Plasmid: pMCSG7 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 magic / References: UniProt: Q83C83
#2: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 301 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.37 Å3/Da / Density % sol: 48.1 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: Protein: 11.0 mg/ml, 0.25M Sodium chloride, 0.01M Tris-HCl pH 8.3, 10mM GDP, Screen: JSCG+ (H11), 0.2M Magnesium chloride, 0.1M Bis-Tris pH 5.5, 25% (w/v) PEG 3350.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Oct 2, 2014
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.76→30 Å / Num. obs: 47308 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 7.2 % / Rmerge(I) obs: 0.051 / Rsym value: 0.051 / Net I/σ(I): 33.8
Reflection shellResolution: 1.76→1.79 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.537 / Mean I/σ(I) obs: 3.9 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
BLU-MAXdata collection
HKL-2000data scaling
PHASERphasing
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2HJC

2hjc
PDB Unreleased entry


Resolution: 1.76→29.05 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.951 / SU B: 3.995 / SU ML: 0.069 / Cross valid method: THROUGHOUT / ESU R: 0.113 / ESU R Free: 0.109 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2044 2386 5.1 %RANDOM
Rwork0.17128 ---
obs0.17295 44856 99.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.181 Å2
Baniso -1Baniso -2Baniso -3
1-0.61 Å20 Å20 Å2
2---0.85 Å20 Å2
3---0.24 Å2
Refinement stepCycle: 1 / Resolution: 1.76→29.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3187 0 56 301 3544
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0193705
X-RAY DIFFRACTIONr_bond_other_d0.0010.023679
X-RAY DIFFRACTIONr_angle_refined_deg1.4731.9865059
X-RAY DIFFRACTIONr_angle_other_deg0.74638428
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.2175477
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.98922.84169
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.23915673
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.3191542
X-RAY DIFFRACTIONr_chiral_restr0.0840.2571
X-RAY DIFFRACTIONr_gen_planes_refined0.020.024301
X-RAY DIFFRACTIONr_gen_planes_other0.0160.02889
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_it2.1142.5161827
X-RAY DIFFRACTIONr_mcbond_other2.1082.5141826
X-RAY DIFFRACTIONr_mcangle_it3.2183.7412331
X-RAY DIFFRACTIONr_mcangle_other3.2173.7432332
X-RAY DIFFRACTIONr_scbond_it2.8122.9591878
X-RAY DIFFRACTIONr_scbond_other2.8162.9611870
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.4764.2872716
X-RAY DIFFRACTIONr_long_range_B_refined7.46721.1974205
X-RAY DIFFRACTIONr_long_range_B_other7.34220.5864087
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.761→1.806 Å
RfactorNum. reflection% reflection
Rfree0.272 152 5 %
Rwork0.223 3055 -
obs--93.55 %
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)
11.19240.14940.07972.38580.44922.053-0.0093-0.0013-0.14940.14430.044-0.16530.185-0.0322-0.03460.0326-0.0084-0.01160.0524-0.02760.04667.6717-6.1517-7.7096
20.0329-0.08310.39160.4094-1.86648.59660.0837-0.03350.01530.01430.18890.03770.0442-0.7555-0.27260.4037-0.01330.00980.272-0.02830.27-2.7291-14.494-28.9591
32.13051.0390.14372.03890.1031.26390.0612-0.09130.04470.149-0.0444-0.11850.0280.0842-0.01680.05310.02380.01570.0360.01330.02997.551-35.0782-25.8203
42.5213-0.73740.68782.943-1.21442.54860.0512-0.0731-0.0065-0.06540.05520.28190.0522-0.2849-0.10640.0649-0.03250.01980.13570.03690.0611-0.2827-11.921-46.0517
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 23
2X-RAY DIFFRACTION1A41 - 164
3X-RAY DIFFRACTION2A24 - 40
4X-RAY DIFFRACTION3A173 - 350
5X-RAY DIFFRACTION4A351 - 434

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