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- PDB-5c9d: Crystal structure of a retropepsin-like aspartic protease from Ri... -

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Basic information

Entry
Database: PDB / ID: 5c9d
TitleCrystal structure of a retropepsin-like aspartic protease from Rickettsia conorii
ComponentsApRick protease
KeywordsHYDROLASE / pepsin / ApRick
Function / homology
Function and homology information


acyltransferase activity / aspartic-type endopeptidase activity / proteolysis / membrane
Similarity search - Function
Clan AA aspartic peptidase, C-terminal / Retropepsin-like domain, bacterial / gag-polyprotein putative aspartyl protease / Cathepsin D, subunit A; domain 1 / Acid Proteases / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Biological speciesRickettsia conorii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.59 Å
AuthorsLi, M. / Gustchina, A. / Cruz, R. / Simoes, M. / Curto, P. / Martinez, J. / Faro, C. / Simoes, I. / Wlodawer, A.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2015
Title: Structure of RC1339/APRc from Rickettsia conorii, a retropepsin-like aspartic protease
Authors: Li, M. / Gustchina, A. / Cruz, R. / Simoes, M. / Curto, P. / Martinez, J. / Faro, C. / Simoes, I. / Wlodawer, A.
History
DepositionJun 26, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 14, 2015Provider: repository / Type: Initial release
Revision 2.0Mar 14, 2018Group: Advisory / Atomic model ...Advisory / Atomic model / Database references / Derived calculations / Non-polymer description / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / entity / entity_poly / entity_poly_seq / entity_src_gen / pdbx_poly_seq_scheme / pdbx_struct_conn_angle / pdbx_struct_oper_list / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_residues / struct_conf / struct_conn / struct_ref / struct_ref_seq / struct_ref_seq_dif / struct_sheet_range / struct_site_gen
Item: _atom_site.label_seq_id / _atom_site_anisotrop.pdbx_label_seq_id ..._atom_site.label_seq_id / _atom_site_anisotrop.pdbx_label_seq_id / _chem_comp.formula / _chem_comp.id / _chem_comp.name / _entity.formula_weight / _entity.pdbx_ec / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_src_gen.pdbx_end_seq_num / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _struct_conf.beg_label_seq_id / _struct_conf.end_label_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_seq_align_beg_ins_code / _struct_ref_seq.seq_align_end / _struct_ref_seq_dif.pdbx_auth_seq_num / _struct_ref_seq_dif.seq_num / _struct_sheet_range.beg_label_seq_id / _struct_sheet_range.end_label_seq_id / _struct_site_gen.label_seq_id
Revision 2.1Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ApRick protease
B: ApRick protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,1343
Polymers30,1112
Non-polymers231
Water905
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1720 Å2
ΔGint-16 kcal/mol
Surface area12520 Å2
MethodPISA
2
A: ApRick protease
B: ApRick protease
hetero molecules

A: ApRick protease
B: ApRick protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,2676
Polymers60,2214
Non-polymers462
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555-x+1/2,y,-z+3/41
Buried area5820 Å2
ΔGint-38 kcal/mol
Surface area22650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.290, 105.290, 90.996
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122

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Components

#1: Protein ApRick protease


Mass: 15055.369 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rickettsia conorii (bacteria) / Gene: RC1339 / Plasmid: pET23a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q92FY8
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.01 Å3/Da / Density % sol: 38.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 1.2 M DL-malic acid, pH 7.0, 2% 1,2-propanol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 24, 2014
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.59→50 Å / Num. all: 8267 / Num. obs: 7658 / % possible obs: 92.5 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.065 / Rsym value: 0.065 / Net I/σ(I): 21.4
Reflection shellResolution: 2.59→2.63 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.457 / Mean I/σ(I) obs: 3.16 / % possible all: 73.1

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.59→41.85 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.927 / SU B: 43.98 / SU ML: 0.42 / Cross valid method: THROUGHOUT / ESU R Free: 0.403 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29768 354 4.6 %RANDOM
Rwork0.22739 ---
obs0.23092 7304 92.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 90.347 Å2
Baniso -1Baniso -2Baniso -3
1-4.2 Å2-0 Å20 Å2
2--4.2 Å20 Å2
3----8.4 Å2
Refinement stepCycle: 1 / Resolution: 2.59→41.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1832 0 1 5 1838
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0191854
X-RAY DIFFRACTIONr_bond_other_d0.0020.021898
X-RAY DIFFRACTIONr_angle_refined_deg1.7071.9782487
X-RAY DIFFRACTIONr_angle_other_deg0.83434353
X-RAY DIFFRACTIONr_dihedral_angle_1_deg10.4665232
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.75224.8179
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.52215358
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.345159
X-RAY DIFFRACTIONr_chiral_restr0.0940.2293
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022057
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02408
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it8.8744.327935
X-RAY DIFFRACTIONr_mcbond_other8.8714.328934
X-RAY DIFFRACTIONr_mcangle_it12.4466.4671166
X-RAY DIFFRACTIONr_mcangle_other12.4446.4671167
X-RAY DIFFRACTIONr_scbond_it10.1925.155917
X-RAY DIFFRACTIONr_scbond_other10.1875.154918
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other14.7997.351322
X-RAY DIFFRACTIONr_long_range_B_refined19.20635.5212033
X-RAY DIFFRACTIONr_long_range_B_other19.20135.5042033
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.588→2.655 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.477 32 -
Rwork0.273 432 -
obs--78.51 %
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)
13.09543.99650.90976.14470.08491.6672-0.48610.4673-0.1999-0.57740.5237-0.39120.0630.2914-0.03760.4681-0.13370.08310.5919-0.15680.3558.08636.482540.9454
22.48060.0151-0.69480.81390.65433.1175-0.19910.5116-0.06030.11320.19520.0222-0.29410.2360.0040.2737-0.0378-0.02070.5263-0.07460.25218.962160.031348.5066
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B110 - 229
2X-RAY DIFFRACTION2A109 - 235

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