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- PDB-3nyy: Crystal structure of a putative glycyl-glycine endopeptidase lytM... -

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Basic information

Entry
Database: PDB / ID: 3nyy
TitleCrystal structure of a putative glycyl-glycine endopeptidase lytM (RUMGNA_02482) from Ruminococcus gnavus ATCC 29149 at 1.60 A resolution
ComponentsPutative glycyl-glycine endopeptidase lytM
KeywordsHYDROLASE / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-BIOLOGY
Function / homology: / LytM, N-terminal domain / : / Peptidase M23 / Peptidase family M23 / Duplicated hybrid motif / metalloendopeptidase activity / membrane / Peptidase, M23 family
Function and homology information
Biological speciesRuminococcus gnavus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.6 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a putative glycyl-glycine endopeptidase lytM (RUMGNA_02482) from Ruminococcus gnavus ATCC 29149 at 1.60 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJul 15, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 15, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 20, 2011Group: Structure summary
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 1.4Nov 27, 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:
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Assembly

Deposited unit
A: Putative glycyl-glycine endopeptidase lytM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6108
Polymers28,9821
Non-polymers1,6287
Water4,846269
1
A: Putative glycyl-glycine endopeptidase lytM
hetero molecules

A: Putative glycyl-glycine endopeptidase lytM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,22016
Polymers57,9652
Non-polymers3,25514
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area3810 Å2
ΔGint-109 kcal/mol
Surface area25070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.336, 61.572, 52.804
Angle α, β, γ (deg.)90.000, 108.500, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-468-

HOH

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Components

#1: Protein Putative glycyl-glycine endopeptidase lytM


Mass: 28982.424 Da / Num. of mol.: 1 / Fragment: sequence database residues 29-279
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ruminococcus gnavus (bacteria) / Gene: RUMGNA_02482 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: A7B4J8
#2: Chemical ChemComp-2PE / NONAETHYLENE GLYCOL


Mass: 414.488 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C18H38O10 / Comment: precipitant*YM
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 269 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE CONSTRUCT (RESIDUES 29-279) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG ...THE CONSTRUCT (RESIDUES 29-279) 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: 2.43 Å3/Da / Density % sol: 49.36 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 30.000000000% PEG-400, 0.200000000M LiSO4, 0.1M Cacodylate pH 6.5, 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: 0.95369,0.97951,0.97905
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jun 9, 2010 / 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
10.953691
20.979511
30.979051
ReflectionResolution: 1.6→28.576 Å / Num. all: 36639 / Num. obs: 36639 / % possible obs: 99.9 % / Redundancy: 3.2 % / Biso Wilson estimate: 16.68 Å2 / Rsym value: 0.079 / Net I/σ(I): 8.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.6-1.643.10.3931.9836926810.393100
1.64-1.693.10.3482.2824026230.348100
1.69-1.743.10.2912.6805225650.291100
1.74-1.793.10.233.3788425090.23100
1.79-1.853.10.1973.8758424090.197100
1.85-1.913.10.1644.3735923370.164100
1.91-1.983.20.1365.4715022680.136100
1.98-2.073.20.1176678521500.117100
2.07-2.163.20.1016.9655620600.101100
2.16-2.263.20.0917.5643020250.091100
2.26-2.393.20.0857.6603419000.085100
2.39-2.533.20.0867.5570017960.086100
2.53-2.73.20.088.1534816730.08100
2.7-2.923.20.0738.6502115770.07399.9
2.92-3.23.20.0639.6460014410.06399.7
3.2-3.583.20.05610.8416013030.05699.7
3.58-4.133.20.05610.5371711640.05699.6
4.13-5.063.20.0531131319780.05399.3
5.06-7.163.20.05910.324037570.05999
7.16-28.5763.10.061913134230.06197.1

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
SHELXphasing
REFMAC5.5.0110refinement
SCALA3.3.15data scaling
PDB_EXTRACT3.1data extraction
MOSFLMdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.6→28.576 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.96 / Occupancy max: 1 / Occupancy min: 0.37 / SU B: 2.724 / SU ML: 0.048 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.076 / ESU R Free: 0.076
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
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. PEG FRAGMENTS (2PE), SULFATE (SO4) MODELED ARE PRESENT IN CRYSTALLIZATION/CRYO CONDITIONS. 3. DENSITY FOR REGION 143-149 IS POOR AND MODEL IS NOT RELIABLE. 4. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 5. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 6. WATERS WERE EXCLUDED FROM AUTOMATIC TLS ASSIGNMENT.
RfactorNum. reflection% reflectionSelection details
Rfree0.1751 1825 5 %RANDOM
Rwork0.1491 ---
obs0.1504 36638 99.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 102.56 Å2 / Biso mean: 22.2315 Å2 / Biso min: 7.68 Å2
Baniso -1Baniso -2Baniso -3
1-1.64 Å20 Å20.77 Å2
2---0.3 Å20 Å2
3----0.85 Å2
Refinement stepCycle: LAST / Resolution: 1.6→28.576 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1994 0 82 269 2345
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0222251
X-RAY DIFFRACTIONr_bond_other_d0.0020.021572
X-RAY DIFFRACTIONr_angle_refined_deg1.5871.9793059
X-RAY DIFFRACTIONr_angle_other_deg1.02233832
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0775283
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.96323.889108
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.34715349
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8791514
X-RAY DIFFRACTIONr_chiral_restr0.1030.2300
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212500
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02471
X-RAY DIFFRACTIONr_mcbond_it1.80131302
X-RAY DIFFRACTIONr_mcbond_other0.4713536
X-RAY DIFFRACTIONr_mcangle_it2.95452112
X-RAY DIFFRACTIONr_scbond_it4.0948949
X-RAY DIFFRACTIONr_scangle_it5.87111932
LS refinement shellResolution: 1.6→1.641 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.237 125 -
Rwork0.223 2550 -
all-2675 -
obs--99.96 %
Refinement TLS params.Method: refined / Origin x: 30.0873 Å / Origin y: 38.2348 Å / Origin z: 0.661 Å
111213212223313233
T0.004 Å20.0018 Å2-0.0044 Å2-0.0022 Å2-0.0026 Å2--0.018 Å2
L0.3325 °20.0423 °2-0.3672 °2-0.3335 °20.0543 °2--1.1882 °2
S0.0074 Å °0.0038 Å °-0.0033 Å °0.0223 Å °0.0102 Å °-0.0048 Å °0.0346 Å °0.0226 Å °-0.0176 Å °

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