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- PDB-4kh9: Crystal structure of a DUF4785 family protein (lpg0956) from Legi... -

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Basic information

Entry
Database: PDB / ID: 4kh9
TitleCrystal structure of a DUF4785 family protein (lpg0956) from Legionella pneumophila subsp. pneumophila str. Philadelphia 1 at 2.00 A resolution
Componentshypothetical protein
KeywordsStructural Genomics / Unknown Function / Three domains protein / PF16024 family / DUF4785 / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homology
Function and homology information


Jelly Rolls - #1370 / Uncharacterised protein PF16024, DUF4785 / Protein of unknown function DUF4785 / : / : / Domain of unknown function (DUF4785) N-terminal domain / Domain of unknown function (DUF4785) central domain / Domain of unknown function (DUF4785) C-terminal domain / Macroglobulin (MG2) domain / Jelly Rolls ...Jelly Rolls - #1370 / Uncharacterised protein PF16024, DUF4785 / Protein of unknown function DUF4785 / : / : / Domain of unknown function (DUF4785) N-terminal domain / Domain of unknown function (DUF4785) central domain / Domain of unknown function (DUF4785) C-terminal domain / Macroglobulin (MG2) domain / Jelly Rolls / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / DUF4785 domain-containing protein
Similarity search - Component
Biological speciesLegionella pneumophila subsp. pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a hypothetical protein (lpg0956) from Legionella pneumophila subsp. pneumophila str. Philadelphia 1 at 2.00 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionApr 30, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 3, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 24, 2014Group: Structure summary
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Revision 1.3Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.4Feb 1, 2023Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_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.pdbx_leaving_atom_flag / _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_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 20, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: hypothetical protein
B: hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,7327
Polymers85,2672
Non-polymers4655
Water4,360242
1
A: hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,6742
Polymers42,6341
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,0585
Polymers42,6341
Non-polymers4254
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.807, 62.975, 70.632
Angle α, β, γ (deg.)64.130, 82.940, 67.170
Int Tables number1
Space group name H-MP1

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Components

#1: Protein hypothetical protein


Mass: 42633.570 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila subsp. pneumophila (bacteria)
Strain: Philadelphia 1 / Gene: lpg0956, YP_094990.1 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): PB1 / References: UniProt: Q5ZWX8
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 242 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE CONSTRUCT (20-392) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...THE CONSTRUCT (20-392) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

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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: 2.32 Å3/Da / Density % sol: 47.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.83
Details: 0.2M calcium acetate, 10.0% polyethylene glycol 8000, 0.1M Imidazole pH 7.83, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97867
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 24, 2013
Details: Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (horizontal focusing)
RadiationMonochromator: single crystal Si(111) bent / Protocol: SAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97867 Å / Relative weight: 1
ReflectionResolution: 2→45.537 Å / Num. obs: 47483 / % possible obs: 88.3 % / Observed criterion σ(I): -3 / Redundancy: 3.66 % / Biso Wilson estimate: 35.553 Å2 / Rmerge(I) obs: 0.043 / Net I/σ(I): 11.89
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
2-2.050.6551.16131186989191.3
2.05-2.110.5071.5126276704189.6
2.11-2.170.4131.8121236475187.4
2.17-2.240.3482.2111115956184.7
2.24-2.310.282.8119226326192
2.31-2.390.2283.4114366039191.7
2.39-2.480.1954.1110465864191.1
2.48-2.580.174.5102355451188.9
2.58-2.70.1425.593014922182.1
2.7-2.830.0977.799445207191.5
2.83-2.980.0681192124837191
2.98-3.160.04715.387534617190.3
3.16-3.380.03321.377684064185.6
3.38-3.650.02328.169273628182.1
3.65-40.0232.770283650189.5
4-4.470.01739.363003286187.8
4.47-5.160.01641.148472532178.5
5.16-6.320.01640.346872410186.9
6.32-8.940.01541.735971862186.2
8.94-45.540.01154.71931997186.2

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SHELXphasing
SHARPphasing
XSCALEJuly 4, 2012data scaling
BUSTER-TNTrefinement
XDSdata reduction
SHELXDphasing
BUSTER2.10.0refinement
RefinementMethod to determine structure: SAD / Resolution: 2→45.537 Å / Cor.coef. Fo:Fc: 0.9494 / Cor.coef. Fo:Fc free: 0.9326 / Occupancy max: 1 / Occupancy min: 0.23 / Cross valid method: THROUGHOUT / σ(F): 0
Details: 1. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED ...Details: 1. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 3.NCS RESTRAINTS WERE IMPOSED BY AUTOBUSTER'S LSSR PROCEDURE (-AUTONCS). 4. CALCIUM, PEG (PEG AND 1PE) ARE PRESENT IN CRYSTALLIZATION/CRYO CONDITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.2207 2410 5.08 %RANDOM
Rwork0.1937 ---
obs0.1951 47471 91.5 %-
Displacement parametersBiso max: 145.86 Å2 / Biso mean: 47.0454 Å2 / Biso min: 18.96 Å2
Baniso -1Baniso -2Baniso -3
1--1.6505 Å23.2343 Å21.3833 Å2
2--0.956 Å20.4465 Å2
3---0.6945 Å2
Refine analyzeLuzzati coordinate error obs: 0.298 Å
Refinement stepCycle: LAST / Resolution: 2→45.537 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5743 0 26 242 6011
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2824SINUSOIDAL4
X-RAY DIFFRACTIONt_trig_c_planes167HARMONIC2
X-RAY DIFFRACTIONt_gen_planes848HARMONIC5
X-RAY DIFFRACTIONt_it5949HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion785SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact6479SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d5949HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg8070HARMONIC21.1
X-RAY DIFFRACTIONt_omega_torsion3.82
X-RAY DIFFRACTIONt_other_torsion2.51
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2266 175 4.9 %
Rwork0.209 3394 -
all0.2098 3569 -
obs--91.5 %
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)
10.36380.1210.33350.42430.12110.9788-0.0282-0.0584-0.02380.03850.01990.01320.01320.07930.0083-0.081-0.00780.0337-0.0857-0.0035-0.023219.66066.09588.8178
20.32770.0982-0.43670.63830.11080.6805-0.0394-0.00660.01510.01130.0030.0056-0.0288-0.03430.0364-0.1029-0.0109-0.0606-0.06610.0133-0.01319.550236.85556.889
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|0 - 390}A0 - 390
2X-RAY DIFFRACTION2{B|0 - 389}B0 - 389

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