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- PDB-6ome: Crystal structure of a probable cytosol aminopeptidase (Leucine a... -

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Basic information

Entry
Database: PDB / ID: 6ome
TitleCrystal structure of a probable cytosol aminopeptidase (Leucine aminopeptidase, LAP) from Chlamydia trachomatis D/UW-3/Cx
ComponentsProbable cytosol aminopeptidase
KeywordsHYDROLASE / NIAID / structural genomics / cytosolic / leucyl aminopeptidase / LAP / zinc-dependent / metalloprotease / Seattle Structural Genomics Center for Infectious Disease / SSGCID
Function / homology
Function and homology information


bacterial leucyl aminopeptidase / leucyl aminopeptidase / metalloaminopeptidase activity / manganese ion binding / cytoplasm
Similarity search - Function
Peptidase M17, leucyl aminopeptidase, N-terminal / Cytosol aminopeptidase family, N-terminal domain / Peptidase M17, leucine aminopeptidase / Cytosol aminopeptidase signature. / Peptidase M17, leucyl aminopeptidase, C-terminal / Peptidase M17, leucine aminopeptidase/peptidase B / Cytosol aminopeptidase family, catalytic domain / Zn peptidases / Aminopeptidase / Macro domain-like ...Peptidase M17, leucyl aminopeptidase, N-terminal / Cytosol aminopeptidase family, N-terminal domain / Peptidase M17, leucine aminopeptidase / Cytosol aminopeptidase signature. / Peptidase M17, leucyl aminopeptidase, C-terminal / Peptidase M17, leucine aminopeptidase/peptidase B / Cytosol aminopeptidase family, catalytic domain / Zn peptidases / Aminopeptidase / Macro domain-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
CARBONATE ION / LEUCINE / Probable cytosol aminopeptidase
Similarity search - Component
Biological speciesChlamydia trachomatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.95 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To Be Published
Title: Crystal structure of a probable cytosol aminopeptidase (Leucine aminopeptidase, LAP) from Chlamydia trachomatis D/UW-3/Cx
Authors: Edwards, T.E. / Dranow, D.M. / Lorimer, D.D. / Horanyi, P.S. / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
History
DepositionApr 18, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 1, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 11, 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_conn_angle / struct_conn
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_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _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_comp_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Probable cytosol aminopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,12515
Polymers55,3571
Non-polymers76714
Water6,557364
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Probable cytosol aminopeptidase
hetero molecules

A: Probable cytosol aminopeptidase
hetero molecules

A: Probable cytosol aminopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)168,37445
Polymers166,0723
Non-polymers2,30142
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area12920 Å2
ΔGint-466 kcal/mol
Surface area51990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)137.960, 137.960, 128.140
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-503-

SO4

21A-503-

SO4

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Probable cytosol aminopeptidase / Leucine aminopeptidase / LAP / Leucyl aminopeptidase


Mass: 55357.449 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlamydia trachomatis (strain D/UW-3/Cx) (bacteria)
Strain: D/UW-3/Cx / Gene: pepA, CT_045 / Production host: Escherichia coli (E. coli)
References: UniProt: O84049, leucyl aminopeptidase, bacterial leucyl aminopeptidase

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Non-polymers , 8 types, 378 molecules

#2: Chemical ChemComp-CO3 / CARBONATE ION / Carbonate


Mass: 60.009 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CO3
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#6: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#7: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#8: Chemical ChemComp-LEU / LEUCINE / Leucine


Type: L-peptide linking / Mass: 131.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO2
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 364 / 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: 3.18 Å3/Da / Density % sol: 61.32 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: ChtrB.00799.a.B1.PW38523 at 16.07 mg/mL with 2 mM L-Leucine set up against MCSG3 screen condition C8: 0.1 M Tris pH 8.5, 3.2 M NaCl; supplemented with 20% ethylene glycol as cryo-protectant; ...Details: ChtrB.00799.a.B1.PW38523 at 16.07 mg/mL with 2 mM L-Leucine set up against MCSG3 screen condition C8: 0.1 M Tris pH 8.5, 3.2 M NaCl; supplemented with 20% ethylene glycol as cryo-protectant; unique puck ID ejv5-2, crystal tracking ID 305504c8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 21, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.95→45.158 Å / Num. obs: 52788 / % possible obs: 100 % / Redundancy: 14.566 % / Biso Wilson estimate: 35.256 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.065 / Rrim(I) all: 0.067 / Χ2: 1.023 / Net I/σ(I): 27.75
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.95-214.820.575.2738440.950.591100
2-2.0614.7810.4526.7437380.9640.468100
2.06-2.1214.7920.3768.0636510.9770.3999.9
2.12-2.1814.8110.3019.8735120.9830.312100
2.18-2.2514.8160.23112.7134460.9910.239100
2.25-2.3314.8230.1915.2633330.9930.196100
2.33-2.4214.7910.15717.8232270.9960.163100
2.42-2.5214.7690.13520.5630980.9960.14100
2.52-2.6314.7630.1124.1229580.9980.114100
2.63-2.7614.7320.09328.4228710.9980.097100
2.76-2.9114.6820.07633.8227240.9980.079100
2.91-3.0814.5810.06538.7625840.9990.067100
3.08-3.314.5320.05445.8524400.9990.056100
3.3-3.5614.3810.04552.122780.9990.047100
3.56-3.914.1990.0457.4521060.9990.042100
3.9-4.3614.0270.03561.72191810.037100
4.36-5.0313.9370.03364.9917150.9990.034100
5.03-6.1713.8020.03463.18147010.035100
6.17-8.7213.3620.03264117610.033100
8.72-45.15811.7020.0363.766990.9990.03198.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHENIX(1.15_3459)refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4zi6

4zi6


Resolution: 1.95→45.158 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 14.9
RfactorNum. reflection% reflection
Rfree0.1714 3108 6.04 %
Rwork0.1427 --
obs0.1444 51435 97.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 112.56 Å2 / Biso mean: 37.8511 Å2 / Biso min: 16.48 Å2
Refinement stepCycle: final / Resolution: 1.95→45.158 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3731 0 38 364 4133
Biso mean--48.72 43.71 -
Num. residues----499
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 22

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.95-1.98050.20321160.16912078219493
1.9805-2.01290.20311440.15852038218293
2.0129-2.04760.19281360.14722101223795
2.0476-2.08490.19861390.15712074221394
2.0849-2.1250.2151020.15262126222894
2.125-2.16830.19081480.15162100224895
2.1683-2.21550.18471370.13922147228497
2.2155-2.2670.17491570.13822148230597
2.267-2.32370.17181370.14172180231798
2.3237-2.38650.17831390.14022182232197
2.3865-2.45680.16241410.14262152229398
2.4568-2.53610.18121520.14462214236699
2.5361-2.62670.17041460.14812181232798
2.6267-2.73180.16011390.14722217235699
2.7318-2.85620.16681410.14652247238899
2.8562-3.00670.16791430.14872227237099
3.0067-3.1950.17631540.14762245239999
3.195-3.44170.17281380.147422562394100
3.4417-3.78780.15841440.135722862430100
3.7878-4.33560.16451550.127123012456100
4.3356-5.46090.14531460.12623392485100
5.4609-45.17010.18861540.157324882642100
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)
18.79543.44816.51988.04926.63417.31620.1139-0.0931-0.0070.0266-0.20060.09270.2093-0.30350.08560.5104-0.11710.08790.577-0.02520.430574.496845.661826.3406
23.3874-0.4576-0.79473.06790.0542.98-0.3035-0.51720.37480.64710.20440.5291-0.2253-0.33590.10050.44630.1786-0.00620.4229-0.06130.467633.700877.813627.3976
30.9721-1.168-0.26963.95210.61820.76340.05490.1361-0.0857-0.3487-0.17530.9639-0.15-0.2320.12880.28520.0709-0.10430.2917-0.05010.411737.632765.066414.0889
40.8815-0.1754-0.07920.73380.10860.7134-0.01760.14630.1831-0.1227-0.05510.0003-0.1613-0.04760.06690.22360.0003-0.05980.17120.04910.190467.260765.593711.7378
52.9870.7797-0.43752.8511-0.09971.0922-0.041-0.00390.28640.0102-0.0865-0.0292-0.2294-0.04150.08310.27190.0389-0.10270.17130.00990.192260.176671.288818.315
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 514 through 514 )A514
2X-RAY DIFFRACTION2chain 'A' and (resid 1 through 135 )A1 - 135
3X-RAY DIFFRACTION3chain 'A' and (resid 136 through 161 )A136 - 161
4X-RAY DIFFRACTION4chain 'A' and (resid 162 through 452 )A162 - 452
5X-RAY DIFFRACTION5chain 'A' and (resid 453 through 499 )A453 - 499

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