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- PDB-5c9f: Crystal structure of a retropepsin-like aspartic protease from Ri... -

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Basic information

Entry
Database: PDB / ID: 5c9f
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 / Resolution: 2 Å
AuthorsLi, M. / Gustchina, A. / Cruz, R. / Simoes, M. / Curto, P. / Martinez, J. / Faro, C. / Simoes, I. / Wlodawer, A.
CitationJournal: Acta Crystallogr. D Biol. Crystallogr. / 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 1.1Apr 18, 2018Group: Data collection / Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / pdbx_prerelease_seq / pdbx_struct_oper_list
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Mar 13, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
C: ApRick protease
D: ApRick protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,38319
Polymers62,8884
Non-polymers49415
Water3,837213
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8020 Å2
ΔGint-175 kcal/mol
Surface area26430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.102, 94.153, 118.636
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A94 - 225
2010B94 - 225
1020A94 - 225
2020C94 - 225
1030A94 - 225
2030D94 - 225
1040B94 - 225
2040C94 - 225
1050B94 - 225
2050D94 - 225
1060C94 - 225
2060D94 - 225

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
ApRick protease


Mass: 15722.117 Da / Num. of mol.: 4
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, Hydrolases
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-NA / SODIUM ION


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


Mass: 18.015 Da / Num. of mol.: 213 / 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: 2.22 Å3/Da / Density % sol: 44.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.8 / Details: 24% PEG4000, 0.2 M lithium sulfate, pH 5.8

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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: Dec 14, 2013
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→50 Å / Num. all: 38668 / Num. obs: 36685 / % possible obs: 94.9 % / Redundancy: 7.4 % / Rsym value: 0.058 / Net I/σ(I): 30.56
Reflection shellResolution: 2→2.03 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 1.74 / % possible all: 64

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementResolution: 2→40 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.93 / SU B: 10.055 / SU ML: 0.146 / Cross valid method: THROUGHOUT / ESU R: 0.198 / ESU R Free: 0.182 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25452 1140 3.1 %RANDOM
Rwork0.19864 ---
obs0.20034 35542 94.87 %-
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: 50.87 Å2
Baniso -1Baniso -2Baniso -3
1--1.2 Å2-0 Å20 Å2
2--1.13 Å20 Å2
3---0.06 Å2
Refinement stepCycle: 1 / Resolution: 2→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4052 0 15 213 4280
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0194145
X-RAY DIFFRACTIONr_bond_other_d0.0090.024196
X-RAY DIFFRACTIONr_angle_refined_deg1.7251.975578
X-RAY DIFFRACTIONr_angle_other_deg1.45439627
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7445518
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.5224.432176
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.5215792
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.1361520
X-RAY DIFFRACTIONr_chiral_restr0.1040.2648
X-RAY DIFFRACTIONr_gen_planes_refined0.010.024600
X-RAY DIFFRACTIONr_gen_planes_other0.0090.02936
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_it9.1676.0912063
X-RAY DIFFRACTIONr_mcbond_other9.1196.0882062
X-RAY DIFFRACTIONr_mcangle_it10.74311.2562572
X-RAY DIFFRACTIONr_mcangle_other10.7611.2652573
X-RAY DIFFRACTIONr_scbond_it13.3448.0012082
X-RAY DIFFRACTIONr_scbond_other13.3327.9852080
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other15.78113.8753002
X-RAY DIFFRACTIONr_long_range_B_refined17.61327.0384477
X-RAY DIFFRACTIONr_long_range_B_other17.6626.9214434
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A72000.12
12B72000.12
21A74810.12
22C74810.12
31A73530.11
32D73530.11
41B72200.12
42C72200.12
51B74020.12
52D74020.12
61C73260.11
62D73260.11
LS refinement shellResolution: 2.001→2.053 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.363 66 -
Rwork0.274 1773 -
obs--65.87 %
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)
11.5782-0.236-0.11341.8021-0.57391.1852-0.0739-0.02560.0292-0.03280.0703-0.1067-0.0389-0.01610.00360.03140.00650.01990.10330.00120.040220.82222.8895-1.7369
22.5288-2.2324-0.80253.29410.23181.0856-0.3859-0.2809-0.33320.35530.2640.36440.13570.10020.1220.16230.0910.05770.11170.02270.134-10.618622.465520.9344
32.68530.60640.86421.5216-0.04062.9261-0.0108-0.1316-0.13030.1104-0.04930.06910.3167-0.20790.06010.1512-0.00140.07960.06860.05290.1086-14.0883-10.258311.0898
42.40370.04530.83111.1909-0.87413.16530.06540.26590.1251-0.05270.055-0.0419-0.41750.1851-0.12040.1343-0.00850.01930.0528-0.01010.065121.34825.253832.2425
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A104 - 225
2X-RAY DIFFRACTION2B104 - 225
3X-RAY DIFFRACTION3C104 - 225
4X-RAY DIFFRACTION4D104 - 225

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