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- PDB-2evr: CRYSTAL STRUCTURE OF A PUTATIVE GAMMA-D-GLUTAMYL-L-DIAMINO ACID E... -

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Basic information

Entry
Database: PDB / ID: 2evr
TitleCRYSTAL STRUCTURE OF A PUTATIVE GAMMA-D-GLUTAMYL-L-DIAMINO ACID ENDOPEPTIDASE (NPUN_R0659) FROM NOSTOC PUNCTIFORME PCC 73102 AT 1.60 A RESOLUTION
ComponentsCOG0791: Cell wall-associated hydrolases (invasion-associated proteins)
KeywordsHYDROLASE / PUTATIVE GAMMA-D-GLUTAMYL-L-DIAMINO ACID ENDOPEPTIDASE / 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 / SH3 type barrels. ...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
Biological speciesNostoc punctiforme (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.6 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
DepositionOct 31, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 22, 2005Provider: 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 1.3Jan 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_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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: COG0791: Cell wall-associated hydrolases (invasion-associated proteins)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9608
Polymers27,5911
Non-polymers3697
Water5,224290
1
A: COG0791: Cell wall-associated hydrolases (invasion-associated proteins)
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)55,92016
Polymers55,1822
Non-polymers73814
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555x,-y,-z+1/21
Unit cell
Length a, b, c (Å)90.470, 90.470, 93.810
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number91
Space group name H-MP4122
Components on special symmetry positions
IDModelComponents
11A-256-

HOH

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Components

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


Mass: 27591.059 Da / Num. of mol.: 1
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: UniProt: B2J9B4
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 290 / 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: 3.19 Å3/Da / Density % sol: 61.16 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop, nanodrop
Details: 2.0M NaCl, 10.0% PEG-6000, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1.0163, 0.9797
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
20.97971
ReflectionResolution: 1.6→28.71 Å / Num. obs: 51615 / % possible obs: 97 % / Redundancy: 4.31 % / Rmerge(I) obs: 0.115 / Net I/σ(I): 9.36
Reflection shell

Rmerge(I) obs: 0.821 / Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)% possible obs (%)Redundancy (%)Mean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.6-1.66903.332.1534136922390
1.66-1.7293.82.75316288321
1.72-1.895.23.57365379616
1.8-1.995.84.54374689835
1.9-2.0297.96.56368949679
2.02-2.1799.18.76357139375
2.17-2.3999.210.81372609782
2.39-2.7399.512.82368369667
2.73-3.4499.816.57621909857
3.4499.723.35741409884

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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
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.6→28.71 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.963 / SU B: 2.435 / SU ML: 0.042 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.06 / ESU R Free: 0.06
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. TENTATIVE MODELS WERE BUILT FOR THE FOLLOWING AREAS WITH POOR DENSITIES: N-TERMINAL A13; C-TERMINAL A233-234. 4. THERE ARE SOME UNUSUAL DENSITIES FEATURES NEAR A114, A116 AREA THAT WERE LEFT UNINTERPRETED.
RfactorNum. reflection% reflectionSelection details
Rfree0.176 2624 5.1 %RANDOM
Rwork0.159 ---
all0.16 ---
obs-48970 99.41 %-
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: 20.031 Å2
Baniso -1Baniso -2Baniso -3
1--0.12 Å20 Å20 Å2
2---0.12 Å20 Å2
3---0.24 Å2
Refinement stepCycle: LAST / Resolution: 1.6→28.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1714 0 22 290 2026
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0221905
X-RAY DIFFRACTIONr_bond_other_d0.0010.021661
X-RAY DIFFRACTIONr_angle_refined_deg1.5081.952614
X-RAY DIFFRACTIONr_angle_other_deg0.81833887
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7665259
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.23424.83993
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.75215298
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.317158
X-RAY DIFFRACTIONr_chiral_restr0.0970.2281
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022222
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02402
X-RAY DIFFRACTIONr_nbd_refined0.2190.2336
X-RAY DIFFRACTIONr_nbd_other0.180.21691
X-RAY DIFFRACTIONr_nbtor_refined0.1890.2957
X-RAY DIFFRACTIONr_nbtor_other0.090.21192
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1820.2214
X-RAY DIFFRACTIONr_metal_ion_refined0.2310.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2670.218
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2410.252
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1890.229
X-RAY DIFFRACTIONr_mcbond_it1.81731171
X-RAY DIFFRACTIONr_mcbond_other0.4983482
X-RAY DIFFRACTIONr_mcangle_it3.15351891
X-RAY DIFFRACTIONr_scbond_it4.4097765
X-RAY DIFFRACTIONr_scangle_it6.1927706
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.302 212 -
Rwork0.253 3466 -
obs--96.97 %
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)
12.504-0.03370.6070.41520.09571.0822-0.0533-0.20220.12570.23030.0386-0.0724-0.0269-0.00290.01470.02070.0229-0.0212-0.05-0.0409-0.051828.581120.437546.632
21.4912-0.12980.14261.80810.53670.6580.0395-0.0469-0.11820.25860.03-0.10910.15420.0093-0.06950.00180.0081-0.0304-0.0526-0.0236-0.043532.5041-0.27836.4309
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

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