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- PDB-3h41: CRYSTAL STRUCTURE OF A NLPC/P60 FAMILY PROTEIN (BCE_2878) FROM BA... -

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Basic information

Entry
Database: PDB / ID: 3h41
TitleCRYSTAL STRUCTURE OF A NLPC/P60 FAMILY PROTEIN (BCE_2878) FROM BACILLUS CEREUS ATCC 10987 AT 1.79 A RESOLUTION
ComponentsNLP/P60 family protein
KeywordsHYDROLASE / NLPC/P60 FAMILY PROTEIN / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-2
Function / homology
Function and homology information


gamma-D-glutamyl-L-lysine dipeptidyl-peptidase / cysteine-type peptidase activity / cell wall organization / cell wall macromolecule catabolic process
Similarity search - Function
Bacterial dipeptidyl-peptidase SH3 domain / Bacterial dipeptidyl-peptidase Sh3 domain / Endopeptidase, NLPC/P60 domain / NlpC/P60 family / endopeptidase domain like (from Nostoc punctiforme) / endopeptidase fold (from Nostoc punctiforme) / SH3 Domains / Papain-like cysteine peptidase superfamily / SH3 type barrels. / Roll ...Bacterial dipeptidyl-peptidase SH3 domain / Bacterial dipeptidyl-peptidase Sh3 domain / Endopeptidase, NLPC/P60 domain / NlpC/P60 family / endopeptidase domain like (from Nostoc punctiforme) / endopeptidase fold (from Nostoc punctiforme) / SH3 Domains / Papain-like cysteine peptidase superfamily / SH3 type barrels. / Roll / Alpha-Beta Complex / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
ALANINE / D-GLUTAMIC ACID / PHOSPHATE ION / Gamma-D-glutamyl-L-lysine dipeptidyl-peptidase
Similarity search - Component
Biological speciesBacillus cereus ATCC 10987 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.79 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2010
Title: Structure of the gamma-D-glutamyl-L-diamino acid endopeptidase YkfC from Bacillus cereus in complex with L-Ala-[gamma]-D-Glu: insights into substrate recognition by NlpC/P60 cysteine peptidases
Authors: Xu, Q. / Abdubek, P. / Astakhova, T. / Axelrod, H.L. / Bakolitsa, C. / Cai, X. / Carlton, D. / Chen, C. / Chiu, H.J. / Chiu, M. / Clayton, T. / Das, D. / Deller, M.C. / Duan, L. / Ellrott, K. ...Authors: Xu, Q. / Abdubek, P. / Astakhova, T. / Axelrod, H.L. / Bakolitsa, C. / Cai, X. / Carlton, D. / Chen, C. / Chiu, H.J. / Chiu, M. / Clayton, T. / Das, D. / Deller, M.C. / Duan, L. / Ellrott, K. / Farr, C.L. / Feuerhelm, J. / Grant, J.C. / Grzechnik, A. / Han, G.W. / Jaroszewski, L. / Jin, K.K. / Klock, H.E. / Knuth, M.W. / Kozbial, P. / Krishna, S.S. / Kumar, A. / Lam, W.W. / Marciano, D. / Miller, M.D. / Morse, A.T. / Nigoghossian, E. / Nopakun, A. / Okach, L. / Puckett, C. / Reyes, R. / Tien, H.J. / Trame, C.B. / van den Bedem, H. / Weekes, D. / Wooten, T. / Yeh, A. / Hodgson, K.O. / Wooley, J. / Elsliger, M.A. / Deacon, A.M. / Godzik, A. / Lesley, S.A. / Wilson, I.A.
History
DepositionApr 17, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 5, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Feb 1, 2023Group: Database references / Derived calculations / Category: database_2 / 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

Downloads & links

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Assembly

Deposited unit
A: NLP/P60 family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,66510
Polymers35,1691
Non-polymers1,4979
Water4,774265
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)95.205, 59.373, 61.333
Angle α, β, γ (deg.)90.000, 103.270, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein NLP/P60 family protein


Mass: 35168.770 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus ATCC 10987 (bacteria) / Gene: BCE_2878, NP_979181.1 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q736M3

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Non-polymers , 5 types, 274 molecules

#2: Chemical ChemComp-ALA / ALANINE


Type: L-peptide linking / Mass: 89.093 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7NO2
#3: Chemical ChemComp-DGL / D-GLUTAMIC ACID


Type: D-peptide linking / Mass: 147.129 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H9NO4
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Chemical
ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 265 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsTHE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE. THE CLONED CONSTRUCT CONTAINS RESIDUES 24-333 OF THE FULL LENGTH PROTEIN.

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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: 2.39 Å3/Da / Density % sol: 48.59 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: 0.2000M NaCl, 50.0000% PEG-200, 0.1M Phosphate Citrate pH 4.2, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97860,0.91837,0.97985
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Mar 27, 2009 / Details: Flat mirror (vertical focusing)
RadiationMonochromator: Single crystal Si(111) bent monochromator (horizontal focusing)
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97861
20.918371
30.979851
ReflectionResolution: 1.79→41.523 Å / Num. obs: 31085 / % possible obs: 97.1 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 16.976 Å2 / Rmerge(I) obs: 0.111 / Net I/σ(I): 9.59
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.78-1.840.7711.89426257886.2
1.84-1.920.5742.512802337897.1
1.92-20.3993.610804285397.8
2-2.110.2994.712341325597.9
2.11-2.240.2146.311745309898.2
2.24-2.410.1717.711574306998.4
2.41-2.660.145912488330098.6
2.66-3.040.10112.211682310798.9
3.04-3.830.05519.611982319198.7
3.83-41.5230.04226.511969325398.4

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0053refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3.006data extraction
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.79→41.523 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.943 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 2.305 / SU ML: 0.071 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.117 / ESU R Free: 0.111
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. 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. 3. RAMACHANDRAN OUTLIER PRO305 IS SUPPORTED BY DENSITY. 4. CYS238 IS OXIDIZED AS CYSTEINE SULFONIC ACID (OCS). 5. THE ALA-D-GAMMA-GLU MODELED IN THE ACTIVE SITE IS BASED ON DENSITY AND FUNCTION OF THE PROTEIN. PHOSPHATE AND PEG FRAGEMENTS ARE PRESENTS IN CRYSTALLIZATION CONDITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.197 1564 5 %RANDOM
Rwork0.163 ---
obs0.165 31083 97.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 65.68 Å2 / Biso mean: 19.859 Å2 / Biso min: 7.59 Å2
Baniso -1Baniso -2Baniso -3
1--0.38 Å20 Å2-0.5 Å2
2---0.49 Å20 Å2
3---0.64 Å2
Refinement stepCycle: LAST / Resolution: 1.79→41.523 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2409 0 80 265 2754
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0222615
X-RAY DIFFRACTIONr_bond_other_d0.0010.021800
X-RAY DIFFRACTIONr_angle_refined_deg1.4991.9733558
X-RAY DIFFRACTIONr_angle_other_deg0.91434421
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5635327
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.37124.336113
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.88915420
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.6711512
X-RAY DIFFRACTIONr_chiral_restr0.0890.2383
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212856
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02500
X-RAY DIFFRACTIONr_mcbond_it1.82331567
X-RAY DIFFRACTIONr_mcbond_other0.5713624
X-RAY DIFFRACTIONr_mcangle_it2.86652557
X-RAY DIFFRACTIONr_scbond_it4.58881048
X-RAY DIFFRACTIONr_scangle_it6.70811990
LS refinement shellResolution: 1.786→1.833 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.279 119 -
Rwork0.25 2083 -
all-2202 -
obs--94.38 %

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