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- PDB-2hbw: Crystal structure of a putative endopeptidase (ava_3396) from ana... -

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Basic information

Entry
Database: PDB / ID: 2hbw
TitleCrystal structure of a putative endopeptidase (ava_3396) from anabaena variabilis atcc 29413 at 1.05 A resolution
ComponentsNLP/P60 protein
KeywordsHYDROLASE / Nlp/p60 family protein / structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


Bacterial dipeptidyl-peptidase SH3 domain / Bacterial dipeptidyl-peptidase Sh3 domain / : / NlpC/P60 domain profile. / 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 ...Bacterial dipeptidyl-peptidase SH3 domain / Bacterial dipeptidyl-peptidase Sh3 domain / : / NlpC/P60 domain profile. / 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
ACETATE ION / Unknown ligand / NLP/P60
Similarity search - Component
Biological speciesAnabaena variabilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.05 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: Structure / Year: 2009
Title: Structural Basis of Murein Peptide Specificity of a gamma-D-Glutamyl-L-Diamino Acid Endopeptidase.
Authors: Xu, Q. / Sudek, S. / McMullan, D. / Miller, M.D. / Geierstanger, B. / Jones, D.H. / Krishna, S.S. / Spraggon, G. / Bursalay, B. / Abdubek, P. / Acosta, C. / Ambing, E. / Astakhova, T. / ...Authors: Xu, Q. / Sudek, S. / McMullan, D. / Miller, M.D. / Geierstanger, B. / Jones, D.H. / Krishna, S.S. / Spraggon, G. / Bursalay, B. / Abdubek, P. / Acosta, C. / Ambing, E. / Astakhova, T. / Axelrod, H.L. / Carlton, D. / Caruthers, J. / Chiu, H.J. / Clayton, T. / Deller, M.C. / Duan, L. / Elias, Y. / Elsliger, M.A. / Feuerhelm, J. / Grzechnik, S.K. / Hale, J. / Won Han, G. / Haugen, J. / Jaroszewski, L. / Jin, K.K. / Klock, H.E. / Knuth, M.W. / Kozbial, P. / Kumar, A. / Marciano, D. / Morse, A.T. / Nigoghossian, E. / Okach, L. / Oommachen, S. / Paulsen, J. / Reyes, R. / Rife, C.L. / Trout, C.V. / van den Bedem, H. / Weekes, D. / White, A. / Wolf, G. / Zubieta, C. / Hodgson, K.O. / Wooley, J. / Deacon, A.M. / Godzik, A. / Lesley, S.A. / Wilson, I.A.
History
DepositionJun 14, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 8, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Jan 25, 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
Remark 999SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...SEQUENCE 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.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NLP/P60 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,6514
Polymers25,5331
Non-polymers1183
Water6,215345
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.480, 86.891, 37.288
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein NLP/P60 protein


Mass: 25533.242 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Anabaena variabilis (bacteria) / Strain: ATCC 29413 / Gene: yp_323898.1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q3M7N3
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 1 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 345 / 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: 2.43 Å3/Da / Density % sol: 49.28 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 4.5
Details: 20.0% 1,4-butanediol, 0.1M Acetate, pH 4.5, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.979008, 0.918370, 0.979291
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 13, 2006 / 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
10.9790081
20.918371
30.9792911
ReflectionResolution: 1.05→35.007 Å / Num. obs: 116587 / % possible obs: 96.7 % / Biso Wilson estimate: 11.574 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 10.83
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique all% possible all
1.05-1.090.6792.3499751102190.4
1.09-1.130.5222.945120987893.3
1.13-1.180.3943.8492931069094.8
1.18-1.240.3294.6501641082496
1.24-1.320.2715.6541241161396.8
1.32-1.420.2017.2527811125797.8
1.42-1.570.1459.6569461207398.8
1.57-1.80.09813.5571621168199.2
1.80.07322.7927701155099.8

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
REFMAC5.2.0019refinement
XSCALEdata scaling
PDB_EXTRACT2data extraction
XDSdata reduction
SHELXphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.05→35.007 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.975 / SU B: 0.716 / SU ML: 0.016 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.021 / ESU R Free: 0.023
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. AN UNKNOWN LIGAND UNL IS LOCATED NEAR THE CATALYTIC RESIDUE CYS 126. DUE TO THE POOR DENSITY, IT CAN NOT BE UNAMBIGUOUSLY IDENTIFIED. ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. AN UNKNOWN LIGAND UNL IS LOCATED NEAR THE CATALYTIC RESIDUE CYS 126. DUE TO THE POOR DENSITY, IT CAN NOT BE UNAMBIGUOUSLY IDENTIFIED. IT RESEMBLES A SHORT PEPTIDE. THERE ARE ADDITIONAL DISORDERED DENSITY AROUND CYS126. 3. BOTH 106 AND 116 SIDE CHAINS ARE DISORDERED ACCORDING TO DENSITY, HOWEVER, ONLY THE MAIN CONFORMATION CAN BE BUILT UNAMBIGUOUSLY, AS A RESULT, SIDE CHAINS OF THESE RESIDUES ARE MODELED WITH PARTIAL OCCUPANCIES. 4. 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 0.7 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 5. N-TERMINAL FROM 1 TO 14 ARE DISORDERED. 6. THERE ARE SOME UNEXPLAINED DENSITIES IN THE SOLVENT AREA.
RfactorNum. reflection% reflectionSelection details
Rfree0.149 5839 5 %RANDOM
Rwork0.125 ---
obs0.126 116513 99.96 %-
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: 9.246 Å2
Baniso -1Baniso -2Baniso -3
1-0.19 Å20 Å20 Å2
2--0.24 Å20 Å2
3----0.43 Å2
Refinement stepCycle: LAST / Resolution: 1.05→35.007 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1675 0 19 345 2039
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0222009
X-RAY DIFFRACTIONr_bond_other_d0.0030.021295
X-RAY DIFFRACTIONr_angle_refined_deg1.9361.962772
X-RAY DIFFRACTIONr_angle_other_deg1.06733197
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0845280
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.50625.11488
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.7715313
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.773158
X-RAY DIFFRACTIONr_chiral_restr0.1210.2298
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022451
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02415
X-RAY DIFFRACTIONr_nbd_refined0.2950.2460
X-RAY DIFFRACTIONr_nbd_other0.2030.21482
X-RAY DIFFRACTIONr_nbtor_refined0.1860.21023
X-RAY DIFFRACTIONr_nbtor_other0.0930.21100
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2290.2264
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3620.218
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1860.235
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.190.230
X-RAY DIFFRACTIONr_mcbond_it2.75331304
X-RAY DIFFRACTIONr_mcbond_other2.1883521
X-RAY DIFFRACTIONr_mcangle_it3.63152087
X-RAY DIFFRACTIONr_scbond_it5.2738795
X-RAY DIFFRACTIONr_scangle_it6.42411685
X-RAY DIFFRACTIONr_rigid_bond_restr2.29133654
X-RAY DIFFRACTIONr_sphericity_free12.9293363
X-RAY DIFFRACTIONr_sphericity_bonded5.88633240
LS refinement shellResolution: 1.05→1.068 Å / Total num. of bins used: 30
RfactorNum. reflection% reflection
Rfree0.296 280 -
Rwork0.264 5415 -
obs-5695 99.96 %

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