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- PDB-4l8k: Crystal structure of a putative peptidase (PARMER_02772) from Par... -

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Basic information

Entry
Database: PDB / ID: 4l8k
TitleCrystal structure of a putative peptidase (PARMER_02772) from Parabacteroides merdae ATCC 43184 at 2.26 A resolution
Componentsputative peptidase
KeywordsHYDROLASE / Peptidase family S41 / PF03572 / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homology
Function and homology information


serine-type peptidase activity
Similarity search - Function
Tricorn protease C1 domain / Tricorn protease C1 domain / Transcription Regulator spoIIAA - #44 / tail specific protease / Tail specific protease / Peptidase family S41 / Transcription Regulator spoIIAA / 2-enoyl-CoA Hydratase; Chain A, domain 1 / 2-enoyl-CoA Hydratase; Chain A, domain 1 / ClpP/crotonase-like domain superfamily ...Tricorn protease C1 domain / Tricorn protease C1 domain / Transcription Regulator spoIIAA - #44 / tail specific protease / Tail specific protease / Peptidase family S41 / Transcription Regulator spoIIAA / 2-enoyl-CoA Hydratase; Chain A, domain 1 / 2-enoyl-CoA Hydratase; Chain A, domain 1 / ClpP/crotonase-like domain superfamily / Alpha-Beta Complex / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Peptidase, S41 family
Similarity search - Component
Biological speciesParabacteroides merdae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.26 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a putative peptidase (PARMER_02772) from Parabacteroides merdae ATCC 43184 at 2.26 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJun 17, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 3, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software
Revision 1.2Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.3Feb 1, 2023Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / 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_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 9, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: putative peptidase
B: putative peptidase
C: putative peptidase
D: putative peptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,07924
Polymers148,0674
Non-polymers2,01220
Water11,151619
1
A: putative peptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,3845
Polymers37,0171
Non-polymers3674
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: putative peptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,5616
Polymers37,0171
Non-polymers5445
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: putative peptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,6928
Polymers37,0171
Non-polymers6757
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: putative peptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4435
Polymers37,0171
Non-polymers4264
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.333, 131.213, 129.056
Angle α, β, γ (deg.)90.000, 90.550, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
putative peptidase


Mass: 37016.754 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Parabacteroides merdae (bacteria) / Strain: ATCC 43184 / Gene: PARMER_02772, ZP_02032754.1 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): PB1 / References: UniProt: A7AH72

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Non-polymers , 5 types, 639 molecules

#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: PO4
#3: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL


Mass: 118.174 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 619 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Sequence detailsTHIS CONSTRUCT (RESIDUES 20-338) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG ...THIS CONSTRUCT (RESIDUES 20-338) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

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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: 2.42 Å3/Da / Density % sol: 49.19 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2M ammonium dihydrogen phosphate, 50.0% 2-methyl-2,4-pentanediol, 4.0% Polypropylene Glycol P 400, 0.1M TRIS pH 8.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
0.918401,1
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.918401 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 18, 2012 / Details: KOHZU: Double Crystal Si(111)
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918401 Å / Relative weight: 1
ReflectionResolution: 2.26→29.652 Å / Num. obs: 65894 / % possible obs: 98.7 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 30.59 Å2 / Rmerge(I) obs: 0.105 / Net I/σ(I): 7.26
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.26-2.340.6131.5247881279098.8
2.34-2.430.4821.8238271231498.9
2.43-2.540.4132.2251741298899.1
2.54-2.680.3132.8261051349399
2.68-2.850.2193.8253161305298.9
2.85-3.070.1515.4249771287999
3.07-3.370.1037.7242111249298.7
3.37-3.860.06312249801295198.1
3.86-4.850.04116.9243161272398.3
4.850.03618.6255891296198.2

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SOLVEphasing
XSCALEMarch 15, 2012data scaling
BUSTER-TNT2.10.0refinement
XDSdata reduction
BUSTER2.10.0refinement
RefinementMethod to determine structure: MAD / Resolution: 2.26→29.652 Å / Cor.coef. Fo:Fc: 0.9485 / Cor.coef. Fo:Fc free: 0.9169 / Occupancy max: 1 / Occupancy min: 0.33 / Cross valid method: THROUGHOUT / σ(F): 0
Details: 1.A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED ...Details: 1.A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 2.ATOM RECORDS CONTAIN SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 3.WATERS WERE EXCLUDED FROM AUTOMATIC TLS ASSIGNMENT. PHOSPHATE (PO4), (4S)-2-METHYL-2,4-PENTANEDIOL (MPD), AND (4R)-2-METHYL-2,4-PENTANEDIOL (MRD),AND CHLORIDE (CL) FROM THE CRYSTALLIZATION/CRYO CONDITIONS HAVE BEEN MODELED INTO THE STRUCTURE. 4.THE REFINEMENT WAS RESTRAINED AGAINST THE MAD PHASES. 4 NCS RESTRAINTS WERE APPLIED USING BUSTER'S LSSR RESTRAINT REPRESENTATION (-AUTONCS).
RfactorNum. reflection% reflectionSelection details
Rfree0.2061 3335 5.07 %RANDOM
Rwork0.1593 ---
obs0.1617 65744 99.88 %-
Displacement parametersBiso max: 115.61 Å2 / Biso mean: 31.8058 Å2 / Biso min: 9.16 Å2
Baniso -1Baniso -2Baniso -3
1--2.0065 Å20 Å2-0.9017 Å2
2---2.5007 Å20 Å2
3---4.5072 Å2
Refine analyzeLuzzati coordinate error obs: 0.244 Å
Refinement stepCycle: LAST / Resolution: 2.26→29.652 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9996 0 122 619 10737
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d4756SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes275HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1543HARMONIC5
X-RAY DIFFRACTIONt_it10478HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1294SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact12547SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d10478HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg14231HARMONIC20.99
X-RAY DIFFRACTIONt_omega_torsion3.55
X-RAY DIFFRACTIONt_other_torsion2.8
LS refinement shellResolution: 2.26→2.32 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2428 219 4.57 %
Rwork0.1914 4575 -
all0.1937 4794 -
obs--99.88 %
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)
10.3592-0.0008-0.18920.4955-0.31761.5347-0.007-0.03720.04440.0484-0.0627-0.0513-0.22840.16820.0697-0.0991-0.0441-0.0103-0.03360.0017-0.046935.308621.802193.34
20.20140.11280.11670.41680.17761.5471-0.0036-0.0287-0.0644-0.010.0099-0.01620.35820.1378-0.0063-0.01560.02090.0066-0.04790.016-0.065929.2424-8.560299.199
30.29210.1021-0.01630.6390.17061.2140.01040.0163-0.02790.0791-0.021-0.00030.1409-0.03930.0106-0.07580.0041-0.0066-0.0333-0.0097-0.037623.408-7.30633.9096
40.19380.0389-0.27720.38120.0052.90510.07040.01620.02730.040.0037-0.0169-0.37620.1582-0.0741-0.0117-0.01790.0051-0.0751-0.0033-0.094430.675922.565130.4489
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|24 - 338}A24 - 338
2X-RAY DIFFRACTION2{B|23 - 337}B23 - 337
3X-RAY DIFFRACTION3{C|23 - 331}C23 - 331
4X-RAY DIFFRACTION4{D|24 - 330}D24 - 330

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