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- PDB-2fg0: Crystal structure of a putative gamma-d-glutamyl-l-diamino acid e... -

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Basic information

Entry
Database: PDB / ID: 2fg0
TitleCrystal structure of a putative gamma-d-glutamyl-l-diamino acid endopeptidase (npun_r0659) from nostoc punctiforme pcc 73102 at 1.79 A resolution
ComponentsCOG0791: Cell wall-associated hydrolases (invasion-associated proteins)
KeywordsHYDROLASE / Nlpc/p60 family / structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


cysteine-type peptidase activity
Similarity search - Function
Bacterial dipeptidyl-peptidase SH3 domain / Bacterial dipeptidyl-peptidase Sh3 domain / : / NlpC/P60 family / NlpC/P60 domain profile. / Endopeptidase, NLPC/P60 domain / 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 family / NlpC/P60 domain profile. / Endopeptidase, NLPC/P60 domain / 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
Biological speciesNostoc punctiforme (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.79 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
DepositionDec 20, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 10, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _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
Revision 1.5Nov 13, 2024Group: Data collection / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: COG0791: Cell wall-associated hydrolases (invasion-associated proteins)
B: COG0791: Cell wall-associated hydrolases (invasion-associated proteins)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,4585
Polymers55,1822
Non-polymers2763
Water7,710428
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2360 Å2
ΔGint-15 kcal/mol
Surface area19420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.080, 125.080, 97.670
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: ARG / End label comp-ID: ARG / Refine code: 2 / Auth seq-ID: 13 - 234 / Label seq-ID: 25 - 246

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein COG0791: Cell wall-associated hydrolases (invasion-associated proteins)


Mass: 27591.059 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nostoc punctiforme (bacteria) / Strain: PCC 73102 / Gene: 53686717 / Production host: Escherichia coli (E. coli) / References: GenBank: 53686717, UniProt: B2J9B4*PLUS
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 428 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.43 Å3/Da / Density % sol: 63.86 %
Description: THE MODEL FROM A SECOND CRYSTAL FORM OF SE-MET CRYSTALS (P 41 2 2, PDB ID 2EVR) WAS USED AS A STARTING MODEL TO SPEED UP THE REFINEMENT. THE STRUCTURE CAN BE SOLVED BY SE-MAD. MORE THAN ...Description: THE MODEL FROM A SECOND CRYSTAL FORM OF SE-MET CRYSTALS (P 41 2 2, PDB ID 2EVR) WAS USED AS A STARTING MODEL TO SPEED UP THE REFINEMENT. THE STRUCTURE CAN BE SOLVED BY SE-MAD. MORE THAN 90 PERCENT OF PROTEIN MODELS CAN BE AUTOMATICALLY TRACED FROM EXPERIMENTAL PHASES ONLY.
Crystal growTemperature: 277 K / pH: 7.5
Details: 1.4M Na3Citrate, 0.1M HEPES, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K, pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1.0163, 0.9798
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Sep 28, 2005
RadiationMonochromator: Double Crystal Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.01631
20.97981
ReflectionResolution: 1.79→29.48 Å / Num. obs: 72488 / % possible obs: 97.5 % / Redundancy: 7.4 % / Rmerge(I) obs: 0.147 / Net I/σ(I): 12.56
Reflection shell

Rmerge(I) obs: 0.01146 / Diffraction-ID: 1

Resolution (Å)% possible obs (%)Redundancy (%)Mean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.79-1.8689.46.52.13850451163089.4
1.86-1.9495.12.7210745914142
1.94-2.03973.9110419913659
2.03-2.1397.75.189677512690
2.13-2.2798.66.4910981414348
2.27-2.44998.5710219813295
2.44-2.6999.210.8710782014008
2.69-3.0799.516.2710443813539
3.07-3.8799.928.0810737513953
3.87-29.4899.639.0710684713941

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0005refinement
XSCALEdata scaling
PDB_EXTRACT1.601data extraction
XDSdata reduction
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.79→29.48 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.963 / SU B: 3.612 / SU ML: 0.056 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.077 / ESU R Free: 0.076
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 0.7 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. THE DIFFERENCE DENSITY MAP NEAR A/B 116 IS NOISY.
RfactorNum. reflection% reflectionSelection details
Rfree0.172 3659 5.1 %RANDOM
Rwork0.154 ---
all0.155 ---
obs-68770 99.55 %-
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: 22.209 Å2
Baniso -1Baniso -2Baniso -3
1-0.37 Å20 Å20 Å2
2--0.37 Å20 Å2
3----0.74 Å2
Refinement stepCycle: LAST / Resolution: 1.79→29.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3426 0 18 428 3872
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0223641
X-RAY DIFFRACTIONr_bond_other_d0.0030.023123
X-RAY DIFFRACTIONr_angle_refined_deg1.5131.9464967
X-RAY DIFFRACTIONr_angle_other_deg0.89137271
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6615466
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.22224.915177
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.4615548
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.6121514
X-RAY DIFFRACTIONr_chiral_restr0.0940.2527
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024231
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02763
X-RAY DIFFRACTIONr_nbd_refined0.2140.2684
X-RAY DIFFRACTIONr_nbd_other0.1850.23296
X-RAY DIFFRACTIONr_nbtor_refined0.1920.21851
X-RAY DIFFRACTIONr_nbtor_other0.0910.22287
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.160.2334
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2240.210
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2670.240
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1610.218
X-RAY DIFFRACTIONr_mcbond_it2.0632383
X-RAY DIFFRACTIONr_mcbond_other0.4953942
X-RAY DIFFRACTIONr_mcangle_it2.89653624
X-RAY DIFFRACTIONr_scbond_it5.07281546
X-RAY DIFFRACTIONr_scangle_it6.639111343
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
1277tight positional0.10.05
1904medium positional0.280.5
1277tight thermal0.260.5
1904medium thermal0.912
LS refinement shellResolution: 1.79→1.841 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.279 273 -
Rwork0.262 4876 -
obs--96.39 %
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)
11.7904-0.5339-0.55291.2285-0.0951.2286-0.16470.3686-0.2115-0.1069-0.00380.0650.2047-0.15080.1685-0.0217-0.0640.01070.0178-0.0567-0.02241.53927.329-0.135
21.28470.13010.04061.06520.43790.8521-0.09470.05910.0615-0.09250.0754-0.03480.02670.06630.0193-0.0441-0.0063-0.0081-0.0521-0.0149-0.032120.55636.81810.454
30.9603-0.74890.36571.883-0.31551.00110.0185-0.12030.08310.2738-0.0678-0.123-0.06250.11120.0493-0.0104-0.0223-0.04010.0013-0.0018-0.051432.54152.76146.788
41.117-0.00720.41251.56710.45921.31570.0474-0.1614-0.09730.2214-0.10680.16130.2405-0.11670.05940.0166-0.02140.0028-0.0256-0.0046-0.02318.51237.02336.039
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA13 - 9025 - 102
2X-RAY DIFFRACTION2AA91 - 234103 - 246
3X-RAY DIFFRACTION3BB13 - 9025 - 102
4X-RAY DIFFRACTION4BB91 - 234103 - 246

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