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- PDB-2pma: Structural Genomics, the crystal structure of a protein Lpg0085 w... -

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Basic information

Entry
Database: PDB / ID: 2pma
TitleStructural Genomics, the crystal structure of a protein Lpg0085 with unknown function (DUF785) from Legionella pneumophila subsp. pneumophila str. Philadelphia 1.
ComponentsUncharacterized protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / APC86035.2 / protein Lpg0085 / DUF785 / Legionella pneumophila subsp. pneumophila str. Philadelphia 1 / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


Putative ATP-dependent zinc protease / Putative ATP-dependent zinc protease / Cathepsin D, subunit A; domain 1 / Acid Proteases / Aspartic peptidase domain superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
ACETATE ION / FORMIC ACID / Putative ATP-dependent zinc protease domain-containing protein
Similarity search - Component
Biological speciesLegionella pneumophila subsp. pneumophila str. Philadelphia 1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.89 Å
AuthorsTan, K. / Mulligan, R. / Moy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of a protein Lpg0085 with unknown function (DUF785) from Legionella pneumophila subsp. pneumophila str. Philadelphia 1.
Authors: Tan, K. / Mulligan, R. / Moy, S. / Joachimiak, A.
History
DepositionApr 20, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 22, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 300 BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 ... BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). AUTHORS STATE THAT THE BIOLOGICAL UNIT OF THIS PROTEIN IS EXPERIMENTALLY UNKNOWN. THE ASSEMBLY SHOWN IN REMARK 350 IS PREDICTED BY THE ANALYSIS OF PROTEIN INTERFACES BASED ON THIS CRYSTAL STRUCTURE.

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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)32,88312
Polymers32,3582
Non-polymers52510
Water2,054114
1
A: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,5408
Polymers16,1791
Non-polymers3617
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,3434
Polymers16,1791
Non-polymers1643
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.711, 81.855, 97.993
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsExperimentally unknown. It could be monomeric based on molecular packing

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Components

#1: Protein Uncharacterized protein / Protein Lpg0085 / Protein DUF785


Mass: 16178.821 Da / Num. of mol.: 2 / Fragment: Residues 26-168
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila subsp. pneumophila str. Philadelphia 1 (bacteria)
Species: Legionella pneumophila / Strain: Philadelphia 1, DSM 7513 / Gene: lpg0085 / Plasmid: pMCSG19 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q5ZZC6
#2: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: CH2O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 114 / 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: 2.58 Å3/Da / Density % sol: 52.4 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 20% PEG1000, 0.2M MgCl2, 0.1M Cacodylate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 19-ID11.14046
SYNCHROTRONAPS 19-ID20.91956, 0.91976, 0.91279
Detector
TypeIDDetectorDateDetails
ADSC QUANTUM 3151CCDAug 3, 2006mirror
ADSC QUANTUM 3152CCDMar 5, 2007mirror
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si 111 crystalSINGLE WAVELENGTHMx-ray1
2Si 111 crystalMADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.140461
20.919561
30.919761
40.912791
ReflectionResolution: 1.89→37.77 Å / Num. all: 27464 / Num. obs: 27464 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7 % / Biso Wilson estimate: 24.8 Å2 / Rmerge(I) obs: 0.045 / Net I/σ(I): 52.7
Reflection shellResolution: 1.89→1.93 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.234 / Mean I/σ(I) obs: 8.2 / % possible all: 97.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
MLPHAREphasing
HKL-3000phasing
RefinementMethod to determine structure: MAD / Resolution: 1.89→37.77 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.943 / SU B: 4.726 / SU ML: 0.072 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.129 / ESU R Free: 0.121 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21301 1381 5 %RANDOM
Rwork0.18439 ---
obs0.18586 26024 99.68 %-
all-26024 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.063 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å20 Å20 Å2
2---0.03 Å20 Å2
3---0.07 Å2
Refinement stepCycle: LAST / Resolution: 1.89→37.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2003 0 35 114 2152
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0222175
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5261.9992947
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8635279
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.27923.7580
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.91615403
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4491513
X-RAY DIFFRACTIONr_chiral_restr0.1230.2357
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021567
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2140.2853
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.310.21459
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1240.2130
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.170.259
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.120.214
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0361.51404
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.69822207
X-RAY DIFFRACTIONr_scbond_it2.5023861
X-RAY DIFFRACTIONr_scangle_it3.8054.5734
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.89→1.942 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.192 101 -
Rwork0.18 1829 -
obs--97.77 %
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)
10.84860.49440.29711.41180.47711.85990.0864-0.0380.06930.0975-0.0329-0.0157-0.0301-0.0243-0.0535-0.1264-0.00250.0055-0.1059-0.0024-0.1331-0.114-18.28611.319
22.10181.14070.03675.8779-0.60811.2811-0.0814-0.12010.0790.1304-0.296-0.8847-0.01590.42050.3774-0.1320.0169-0.049-0.03590.166-0.010313.222-35.8723.481
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA23 - 941 - 72
2X-RAY DIFFRACTION1AA110 - 16688 - 144
3X-RAY DIFFRACTION2BB23 - 921 - 70
4X-RAY DIFFRACTION2BB110 - 16688 - 144

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