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- PDB-3na6: Crystal structure of a succinylglutamate desuccinylase (TM1040_26... -

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Basic information

Entry
Database: PDB / ID: 3na6
TitleCrystal structure of a succinylglutamate desuccinylase (TM1040_2694) from SILICIBACTER SP. TM1040 at 2.00 A resolution
ComponentsSuccinylglutamate desuccinylase/aspartoacylase
KeywordsHYDROLASE / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides / hydrolase activity, acting on ester bonds / metal ion binding
Similarity search - Function
N-alpha-acetyl diaminobutyrate deacetylase DoeB / N-alpha-acetyl diaminobutyric acid deacetylase-like / : / : / Succinylglutamate desuccinylase/Aspartoacylase catalytic domain / AstE/AspA barrel-sandwich hybrid domain / Zn peptidases / Aminopeptidase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Succinylglutamate desuccinylase/aspartoacylase
Similarity search - Component
Biological speciesRuegeria sp. TM1040 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a succinylglutamate desuccinylase (TM1040_2694) from SILICIBACTER SP. TM1040 at 2.00 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJun 1, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 28, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Jul 17, 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 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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 20, 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:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Succinylglutamate desuccinylase/aspartoacylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,4614
Polymers36,2631
Non-polymers1983
Water5,639313
1
A: Succinylglutamate desuccinylase/aspartoacylase
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)218,76524
Polymers217,5796
Non-polymers1,18618
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/21
crystal symmetry operation11_655-x+y+1,y,-z+1/21
crystal symmetry operation12_555x,x-y,-z+1/21
Buried area22300 Å2
ΔGint-188 kcal/mol
Surface area67490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.773, 99.773, 137.179
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-631-

HOH

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Components

#1: Protein Succinylglutamate desuccinylase/aspartoacylase


Mass: 36263.230 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ruegeria sp. TM1040 (bacteria) / Gene: TM1040_2694 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q1GD40
#2: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 313 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
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.

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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: 2.72 Å3/Da / Density % sol: 54.74 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.2000M NaCl, 30.0000% PEG-3000, 0.1M TRIS pH 7.0, 0.006 M Calcium Chloride, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.91837,0.97922,0.97905
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Mar 11, 2010 / Details: Flat collimating mirror, toroid focusing mirror
RadiationMonochromator: Double crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.979221
30.979051
ReflectionResolution: 2→29.487 Å / Num. obs: 27876 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 28.032 Å2 / Rmerge(I) obs: 0.157 / Net I/σ(I): 11.56
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2-2.070.0131.837250490396.6
2.07-2.150.0132.338330499699.8
2.15-2.250.0132.840682529399.9
2.25-2.370.0133.840453525099.9
2.37-2.520.0134.840314520899.8
2.52-2.710.0136.639233506699.9
2.71-2.990.0139.841142529999.8
2.99-3.420.01316.3400845149100
3.42-4.30.01327.7399425138100
4.3-29.4870.01339.140549523299.6

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0110refinement
PHENIXrefinement
SOLVEphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3.006data extraction
XDSdata reduction
RefinementMethod to determine structure: MAD / Resolution: 2→29.487 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.951 / Occupancy max: 1 / Occupancy min: 0.37 / SU B: 5.725 / SU ML: 0.085 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.131
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 ...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) ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS.(4) WATERS WERE EXCLUDED FROM AUTOMATIC TLS ASSIGNMENT. (5) CHLORIDE (CL), CALCIUM (CA) AND TRIS (TRS) IONS ARE MODELED FROM CRYSTALLIZATION CONDITION. (6) REGION OF RESIDUES 251-256 CONTAINS POOR ELECTRON DENSITY. MODEL AT THIS REGION IS NOT RELIABLE.
RfactorNum. reflection% reflectionSelection details
Rfree0.195 1397 5 %RANDOM
Rwork0.161 ---
obs0.163 27844 99.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 105.44 Å2 / Biso mean: 29.563 Å2 / Biso min: 11.38 Å2
Baniso -1Baniso -2Baniso -3
1-0.92 Å20.46 Å20 Å2
2--0.92 Å20 Å2
3----1.38 Å2
Refinement stepCycle: LAST / Resolution: 2→29.487 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2493 0 10 313 2816
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0222650
X-RAY DIFFRACTIONr_bond_other_d0.0010.021787
X-RAY DIFFRACTIONr_angle_refined_deg1.5131.9663611
X-RAY DIFFRACTIONr_angle_other_deg0.89434353
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5265346
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.24223.75120
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.02315424
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.7621521
X-RAY DIFFRACTIONr_chiral_restr0.0940.2396
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213049
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02542
X-RAY DIFFRACTIONr_mcbond_it1.72431690
X-RAY DIFFRACTIONr_mcbond_other0.4963687
X-RAY DIFFRACTIONr_mcangle_it2.81752728
X-RAY DIFFRACTIONr_scbond_it5.168960
X-RAY DIFFRACTIONr_scangle_it7.27911883
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.254 120 -
Rwork0.216 1846 -
all-1966 -
obs--98.35 %
Refinement TLS params.Method: refined / Origin x: 31.6428 Å / Origin y: 11.7766 Å / Origin z: 18.1997 Å
111213212223313233
T0.0272 Å2-0.001 Å20.0036 Å2-0.0194 Å2-0.0181 Å2--0.0177 Å2
L0.1511 °2-0.129 °2-0.0362 °2-0.2766 °20.2195 °2--0.569 °2
S0.0011 Å °0.0131 Å °-0.0178 Å °-0.0394 Å °-0.0487 Å °0.0426 Å °0.0179 Å °-0.0621 Å °0.0476 Å °

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