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- PDB-4gyt: Crystal structure of lpg0076 protein from Legionella pneumophila -

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Basic information

Entry
Database: PDB / ID: 4gyt
TitleCrystal structure of lpg0076 protein from Legionella pneumophila
Componentsuncharacterized protein
KeywordsStructural Genomics / Unknown Function / PSI-Biology / Midwest Center for Structural Genomics / MCSG / predicted Legionella effector
Function / homologyYgfB uncharacterised protein family PF03695 / YgfB-like / YgfB-like superfamily / Uncharacterised protein family (UPF0149) / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha / cytosol / YecA family protein
Function and homology information
Biological speciesLegionella pneumophila subsp. pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.047 Å
AuthorsMichalska, K. / Xu, X. / Cui, H. / Savchenko, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal structure of lpg0076 protein from Legionella pneumophila
Authors: Michalska, K. / Xu, X. / Cui, H. / Savchenko, A. / Joachimiak, A.
History
DepositionSep 5, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 26, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_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: uncharacterized protein
B: uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,7104
Polymers43,6642
Non-polymers462
Water2,198122
1
A: uncharacterized protein
hetero molecules

B: uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,7104
Polymers43,6642
Non-polymers462
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y+1/2,-z+1/21
Buried area1710 Å2
ΔGint-36 kcal/mol
Surface area17550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.847, 85.872, 103.845
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 uncharacterized protein


Mass: 21832.152 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila subsp. pneumophila (bacteria)
Strain: str. Philadelphia 1 / Gene: lpg0076 / Plasmid: p15Tv lic / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL / References: UniProt: Q5ZZD5
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 122 / 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: 2.65 Å3/Da / Density % sol: 53.53 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1M Bis-Tris, 0.2M ammonium acetate, 27% PEG3350, 5% Jeff M-600, 1/280 trypsin , pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97929 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 11, 2012 / Details: mirrors
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97929 Å / Relative weight: 1
ReflectionResolution: 2.047→30 Å / Num. all: 29913 / Num. obs: 28918 / % possible obs: 96.7 % / Observed criterion σ(I): -3 / Redundancy: 8.8 % / Biso Wilson estimate: 38.5 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 27.4
Reflection shellResolution: 2.05→2.09 Å / Redundancy: 8.8 % / Rmerge(I) obs: 0.752 / Mean I/σ(I) obs: 3.5 / Num. unique all: 1417 / % possible all: 97.3

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
SHELXmodel building
MLPHAREphasing
DMmodel building
BUCCANEERmodel building
ARP/wARPmodel building
Cootmodel building
PHENIX(phenix.refine: dev_1096)refinement
HKL-3000data reduction
HKL-3000data scaling
SHELXphasing
DMphasing
BUCCANEERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.047→28.789 Å / SU ML: 0.16 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 21.48 / Stereochemistry target values: ML
Details: HYDROGEN ATOMS HAVE BEEN ADDED AT THE RIDING POSITIONS; THE PROTEIN WAS SUBJECTED TO IN SITU PROTEOLYSIS, THEREFORE THE EXACT LENGTH OF THE CRYSTALLIZED POLYPEPTIDE COULD NOT BE DETERMINED
RfactorNum. reflection% reflectionSelection details
Rfree0.2129 1454 5.04 %random
Rwork0.1692 ---
all0.173 28862 --
obs0.1713 28862 96.44 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.047→28.789 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2798 0 2 122 2922
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0122918
X-RAY DIFFRACTIONf_angle_d1.2033942
X-RAY DIFFRACTIONf_dihedral_angle_d17.3421082
X-RAY DIFFRACTIONf_chiral_restr0.069426
X-RAY DIFFRACTIONf_plane_restr0.005530
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0472-2.12030.25481490.20912666X-RAY DIFFRACTION96
2.1203-2.20520.24121480.20132741X-RAY DIFFRACTION98
2.2052-2.30550.23571410.18752736X-RAY DIFFRACTION98
2.3055-2.4270.2341560.17312732X-RAY DIFFRACTION98
2.427-2.5790.25421490.17252739X-RAY DIFFRACTION97
2.579-2.77790.22291340.19132752X-RAY DIFFRACTION97
2.7779-3.05720.27171510.20192726X-RAY DIFFRACTION96
3.0572-3.49890.24611320.17822733X-RAY DIFFRACTION96
3.4989-4.40580.16771570.14612744X-RAY DIFFRACTION95
4.4058-28.79130.1911370.15642839X-RAY DIFFRACTION93
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)
13.6434-0.42730.45093.4026-0.48463.16310.1267-0.11920.1346-0.0557-0.2343-0.3324-0.21310.3723-0.01310.237-0.0487-0.02250.2503-0.00850.209417.007529.283818.4421
20.297-0.19450.17790.76370.40010.5432-0.1435-0.6125-0.82970.88750.3447-0.5910.33550.47190.04980.30250.1097-0.0560.53980.0720.653824.614817.475522.9323
31.44340.481-0.20010.6326-0.4451.3499-0.0314-0.34060.22430.2615-0.0443-0.1723-0.44630.0962-0.00010.3021-0.0369-0.06650.3011-0.04150.236113.230634.60924.9391
42.0753-1.2614-0.95611.4131-0.7653.09910.06090.31590.2413-0.4117-0.1605-0.2562-0.22650.23180.00090.40340.00790.03370.31630.01730.284117.001437.09368.0537
52.1409-0.49091.19924.39460.70472.9582-0.03790.7378-0.1444-0.7791-0.10110.5319-0.214-0.50740.0130.50090.0235-0.18050.4625-0.07670.36071.776533.01647.0913
61.73780.21040.98541.19050.95051.17170.2850.58820.6906-0.2869-0.0465-0.074-1.219-0.09390.00210.60010.089-0.00520.39050.05920.448610.727545.85486.5921
70.6394-0.6125-0.57720.60810.44750.59020.20120.3773-0.0266-0.0457-0.17130.5822-0.1718-0.53080.00430.2882-0.0191-0.09060.293-0.06160.374-4.019634.340820.2922
82.3069-0.98810.92171.76470.42122.2857-0.07911.1177-0.8398-0.48310.1033-0.70320.59150.71370.0210.4461-0.06560.05460.6015-0.03110.30978.96492.53472.1726
91.01180.86221.28731.73780.56361.9374-0.14440.24490.2823-0.1558-0.0313-0.0137-0.0042-0.0158-0.00020.2072-0.0028-0.02310.27820.02280.26067.03269.013114.113
100.9213-0.04710.98030.40880.44981.5452-0.2380.26910.3132-0.219-0.04840.2327-0.88920.13760.00040.525-0.0774-0.1350.38910.05120.35512.074811.85912.0666
112.04571.0751.57832.0911-0.22582.2198-0.01080.3969-1.2951-0.2976-0.1007-0.08230.4410.06690.02730.41810.0322-0.00150.2895-0.07620.43215.9802-4.342113.154
122.47090.97921.79233.0156-0.32051.81570.08210.0826-0.08540.13020.0166-0.74370.25820.64790.01990.30010.0597-0.06380.36950.02140.417516.50193.581521.8672
131.4287-0.65450.78291.06160.5571.5165-0.0934-0.1005-0.4423-0.07930.2106-0.86760.62291.29140.02220.49860.26590.02160.6327-0.05250.803723.0021-5.694816.4996
141.18060.788-0.0560.8436-0.52810.78960.0496-0.469-0.21160.14960.055-0.05060.1224-0.3716-0.00090.30370.0107-0.07060.30440.05360.30455.41011.419428.9316
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 7:52)
2X-RAY DIFFRACTION2(chain A and resid 53:65)
3X-RAY DIFFRACTION3(chain A and resid 66:91)
4X-RAY DIFFRACTION4(chain A and resid 92:116)
5X-RAY DIFFRACTION5(chain A and resid 117:150)
6X-RAY DIFFRACTION6(chain A and resid 151:173)
7X-RAY DIFFRACTION7(chain A and resid 174:183)
8X-RAY DIFFRACTION8(chain B and resid 7:27)
9X-RAY DIFFRACTION9(chain B and resid 28:52)
10X-RAY DIFFRACTION10(chain B and resid 53:77)
11X-RAY DIFFRACTION11(chain B and resid 78:98)
12X-RAY DIFFRACTION12(chain B and resid 99:139)
13X-RAY DIFFRACTION13(chain B and resid 140:172)
14X-RAY DIFFRACTION14(chain B and resid 173:183)

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