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- PDB-3ij3: 1.8 Angstrom Resolution Crystal Structure of Cytosol Aminopeptida... -

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Basic information

Entry
Database: PDB / ID: 3ij3
Title1.8 Angstrom Resolution Crystal Structure of Cytosol Aminopeptidase from Coxiella burnetii
ComponentsCytosol aminopeptidase
KeywordsHYDROLASE / Cytosol Aminopeptidase / pepb / Peptidase M17 family / idp01962 / Aminopeptidase / Manganese / Metal-binding / Protease / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


leucyl aminopeptidase / metalloaminopeptidase activity / manganese ion binding / peptidase activity / proteolysis / cytoplasm
Similarity search - Function
: / M17 aminopeptidase, N-terminal domain / Cytosol aminopeptidase signature. / Peptidase M17, leucyl aminopeptidase, C-terminal / Peptidase M17, leucine aminopeptidase/peptidase B / Cytosol aminopeptidase family, catalytic domain / Leucine Aminopeptidase, subunit E, domain 1 / Leucine Aminopeptidase, subunit E; domain 1 / Zn peptidases / Aminopeptidase ...: / M17 aminopeptidase, N-terminal domain / Cytosol aminopeptidase signature. / Peptidase M17, leucyl aminopeptidase, C-terminal / Peptidase M17, leucine aminopeptidase/peptidase B / Cytosol aminopeptidase family, catalytic domain / Leucine Aminopeptidase, subunit E, domain 1 / Leucine Aminopeptidase, subunit E; domain 1 / Zn peptidases / Aminopeptidase / Macro domain-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Cytosol aminopeptidase
Similarity search - Component
Biological speciesCoxiella burnetii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsMinasov, G. / Halavaty, A. / Shuvalova, L. / Dubrovska, I. / Winsor, J. / Papazisi, L. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: TO BE PUBLISHED
Title: 1.8 Angstrom Resolution Crystal Structure of Cytosol Aminopeptidase from Coxiella burnetii
Authors: Minasov, G. / Halavaty, A. / Shuvalova, L. / Dubrovska, I. / Winsor, J. / Papazisi, L. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionAug 3, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 11, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 6, 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 / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cytosol aminopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,38617
Polymers53,6881
Non-polymers1,69816
Water7,332407
1
A: Cytosol aminopeptidase
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)332,318102
Polymers322,1296
Non-polymers10,18896
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_765-y+2,x-y+1,z1
crystal symmetry operation3_675-x+y+1,-x+2,z1
crystal symmetry operation4_556y,x,-z+11
crystal symmetry operation5_676x-y+1,-y+2,-z+11
crystal symmetry operation6_766-x+2,-x+y+1,-z+11
Buried area43430 Å2
ΔGint-621 kcal/mol
Surface area98000 Å2
MethodPISA
2
A: Cytosol aminopeptidase
hetero molecules

A: Cytosol aminopeptidase
hetero molecules

A: Cytosol aminopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)166,15951
Polymers161,0653
Non-polymers5,09448
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_765-y+2,x-y+1,z1
crystal symmetry operation3_675-x+y+1,-x+2,z1
Buried area15660 Å2
ΔGint-281 kcal/mol
Surface area55050 Å2
MethodPISA
3
A: Cytosol aminopeptidase
hetero molecules

A: Cytosol aminopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,77334
Polymers107,3762
Non-polymers3,39632
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556y,x,-z+11
Buried area6880 Å2
ΔGint-160 kcal/mol
Surface area39900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.803, 112.803, 78.089
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321
Components on special symmetry positions
IDModelComponents
11A-462-

SO4

21A-462-

SO4

31A-872-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Cytosol aminopeptidase


Mass: 53688.227 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Coxiella burnetii (bacteria) / Strain: RSA 493 / Gene: CBU_0572, pepB / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-DE3 / References: UniProt: Q83DX0, leucyl aminopeptidase

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Non-polymers , 8 types, 423 molecules

#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-LI / LITHIUM ION


Mass: 6.941 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Li
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#7: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#8: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 407 / 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: 2.67 Å3/Da / Density % sol: 53.96 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Protein solution at 7.0 mg/mL, 0.5M Sodium cloride, Screen solution JCSG+D7, 0.2M Lithium sulfate, 0.1M Tris, 40% v/v PEG 400, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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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 300 mm CCD / Detector: CCD / Date: Jul 7, 2009 / Details: Beryllium lenses
RadiationMonochromator: Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. all: 53424 / Num. obs: 53424 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 8.9 % / Biso Wilson estimate: 24.2 Å2 / Rmerge(I) obs: 0.087 / Net I/σ(I): 24.3
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 8.5 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 4.6 / Num. unique all: 2656 / % possible all: 100

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Processing

Software
NameVersionClassification
Blu-IceMaxdata collection
PHASERphasing
REFMAC5.5.0088refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1LAM

1lam


Resolution: 1.8→28.21 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.962 / SU B: 3.861 / SU ML: 0.057 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Individual Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.098 / ESU R Free: 0.095 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17685 2711 5.1 %RANDOM
Rwork0.14705 ---
all0.14855 50601 --
obs0.14855 50601 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 15.878 Å2
Baniso -1Baniso -2Baniso -3
1--0.14 Å2-0.07 Å20 Å2
2---0.14 Å20 Å2
3---0.21 Å2
Refinement stepCycle: LAST / Resolution: 1.8→28.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3581 0 105 407 4093
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0224027
X-RAY DIFFRACTIONr_bond_other_d0.0010.022789
X-RAY DIFFRACTIONr_angle_refined_deg1.5081.9915472
X-RAY DIFFRACTIONr_angle_other_deg0.90236810
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.525509
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.03724.111180
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.84315669
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.6571528
X-RAY DIFFRACTIONr_chiral_restr0.1050.2586
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214527
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02805
X-RAY DIFFRACTIONr_mcbond_it1.111.52450
X-RAY DIFFRACTIONr_mcbond_other0.341.5975
X-RAY DIFFRACTIONr_mcangle_it1.95823971
X-RAY DIFFRACTIONr_scbond_it2.94931577
X-RAY DIFFRACTIONr_scangle_it4.754.51501
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.201 211 -
Rwork0.168 3700 -
obs-3700 100 %
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)
10.7835-0.7890.60781.0954-0.50840.5330.0628-0.0498-0.108-0.03280.01550.02040.0769-0.0086-0.07830.13810.0136-0.00410.12870.0190.154968.563852.291729.945
20.5293-0.13490.04921.0730.05680.38580.00960.0185-0.008-0.0879-0.01020.00730.0466-0.01840.00050.0362-0.00770.00080.0246-0.00050.000845.930577.232114.2004
30.5341-0.24140.01340.66850.02750.5637-0.0379-0.0477-0.03060.07030.03460.0320.0429-0.00930.00330.0627-0.00770.01340.05540.01020.041542.327671.267329.2207
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 159
2X-RAY DIFFRACTION2A160 - 341
3X-RAY DIFFRACTION3A342 - 458

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