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- PDB-3fmc: CRYSTAL STRUCTURE OF a putative succinylglutamate desuccinylase /... -

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Basic information

Entry
Database: PDB / ID: 3fmc
TitleCRYSTAL STRUCTURE OF a putative succinylglutamate desuccinylase / aspartoacylase family protein (SAMA_0604) FROM SHEWANELLA AMAZONENSIS SB2B AT 1.80 A RESOLUTION
ComponentsPutative succinylglutamate desuccinylase / aspartoacylase
KeywordsHYDROLASE / PUTATIVE SUCCINYLGLUTAMATE DESUCCINYLASE / ASPARTOACYLASE / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-2
Function / homology
Function and homology information


hydrolase activity, acting on ester bonds / metal ion binding
Similarity search - Function
: / : / Succinylglutamate desuccinylase/Aspartoacylase catalytic domain / AstE/AspA barrel-sandwich hybrid domain / RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain / Zn peptidases / Aminopeptidase / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / 3-Layer(aba) Sandwich ...: / : / Succinylglutamate desuccinylase/Aspartoacylase catalytic domain / AstE/AspA barrel-sandwich hybrid domain / RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain / Zn peptidases / Aminopeptidase / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Succinylglutamate desuccinylase/Aspartoacylase catalytic domain-containing protein
Similarity search - Component
Biological speciesShewanella amazonensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of putative succinylglutamate desuccinylase / aspartoacylase (YP_926482.1) from Shewanella amazonensis SB2B at 1.80 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionDec 19, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 6, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Oct 25, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_struct_assembly_auth_evidence / software / Item: _software.classification / _software.name
Revision 1.3Jul 24, 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 / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 30, 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: _pdbx_entry_details.has_protein_modification / _struct_ncs_dom_lim.beg_auth_comp_id ..._pdbx_entry_details.has_protein_modification / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative succinylglutamate desuccinylase / aspartoacylase
B: Putative succinylglutamate desuccinylase / aspartoacylase
C: Putative succinylglutamate desuccinylase / aspartoacylase
D: Putative succinylglutamate desuccinylase / aspartoacylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)166,66517
Polymers165,4484
Non-polymers1,21713
Water31,6881759
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17370 Å2
ΔGint-100.2 kcal/mol
Surface area48740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.279, 140.101, 164.170
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: VAL / Beg label comp-ID: VAL / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: 6 / Auth seq-ID: 3 - 367 / Label seq-ID: 4 - 368

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD
DetailsSTATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF A TETRAMER AS A SIGNIFICANT OLIGOMERIZATION STATE.

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Components

#1: Protein
Putative succinylglutamate desuccinylase / aspartoacylase


Mass: 41361.953 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella amazonensis (bacteria) / Strain: SB2B / Gene: Sama_0604, YP_926482.1 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: A1S356
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1759 / 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: 3.42 Å3/Da / Density % sol: 63.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: NANODROP, 1.5M Li2SO4, 0.1M HEPES pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.94645, 0.97967
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 11, 2008 / Details: Adjustable focusing mirrors in K-B geometry
RadiationMonochromator: Si(111) Double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.946451
20.979671
ReflectionResolution: 1.8→29.735 Å / Num. obs: 184530 / % possible obs: 88.4 % / Redundancy: 4.8 % / Biso Wilson estimate: 18.527 Å2 / Rmerge(I) obs: 0.105 / Rsym value: 0.105 / Net I/σ(I): 5.074
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.8-1.853.60.5721.338289106740.57269.7
1.85-1.93.60.431.837572103810.4369.3
1.9-1.953.70.3622.137228101270.36269.8
1.95-2.013.90.3382.253197135320.33895.8
2.01-2.0840.2742.751754130890.27495.5
2.08-2.1540.2333.250057126190.23395.3
2.15-2.2340.2053.548194121300.20594.9
2.23-2.3240.179446512116710.17994.9
2.32-2.4340.1584.444683111530.15894.4
2.43-2.5540.139542874106490.13994.1
2.55-2.6850.1464.750153100950.14693.7
2.68-2.855.40.1345.15176395300.13493.3
2.85-3.046.20.1175.65572189370.11792.9
3.04-3.296.80.16.35587382750.192.4
3.29-3.66.80.0847.45158275930.08491.9
3.6-4.026.80.0777.74654968510.07791.3
4.02-4.656.80.0728.24091060300.07290.6
4.65-5.696.80.0718.23467750780.07189.9
5.69-8.056.90.07382699839340.07388.8
8.05-29.7356.70.0667.21452721820.06685.5

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
SCALA3.2.5data scaling
PDB_EXTRACT3.006data extraction
MAR345CCDdata collection
MOSFLMdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.8→29.735 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.954 / Occupancy max: 1 / Occupancy min: 0.25 / SU B: 1.98 / SU ML: 0.062 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.1 / ESU R Free: 0.1
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 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. SULFATE (SO4) IONS FROM CRYSTALLIZATION CONDITION AND GLYCEROL (GOL) MOLECULES FROM CRYO SOLUTION ARE MODELED. 4. RAMACHANDRAN OUTLIER RESIDUES 174 IN ALL FOUR CHAINS ARE SUPPORTED BY ELECTRON DENSITY.
RfactorNum. reflection% reflectionSelection details
Rfree0.187 9270 5 %RANDOM
Rwork0.155 ---
obs0.157 184450 88.15 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 94.21 Å2 / Biso mean: 22.582 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-0.22 Å20 Å20 Å2
2---0.4 Å20 Å2
3---0.19 Å2
Refinement stepCycle: LAST / Resolution: 1.8→29.735 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11443 0 73 1759 13275
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.02212274
X-RAY DIFFRACTIONr_bond_other_d0.0010.028227
X-RAY DIFFRACTIONr_angle_refined_deg1.6841.9716745
X-RAY DIFFRACTIONr_angle_other_deg0.978320059
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.60851553
X-RAY DIFFRACTIONr_dihedral_angle_2_deg25.90723.521551
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.879152009
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.1921581
X-RAY DIFFRACTIONr_chiral_restr0.1070.21835
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213903
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022522
X-RAY DIFFRACTIONr_nbd_refined0.2060.22435
X-RAY DIFFRACTIONr_nbd_other0.1980.29177
X-RAY DIFFRACTIONr_nbtor_refined0.1770.25937
X-RAY DIFFRACTIONr_nbtor_other0.0870.26335
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1590.21396
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.010.23
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0730.26
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2830.254
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1690.239
X-RAY DIFFRACTIONr_mcbond_it2.03738179
X-RAY DIFFRACTIONr_mcbond_other0.55533070
X-RAY DIFFRACTIONr_mcangle_it2.711512222
X-RAY DIFFRACTIONr_scbond_it4.74385180
X-RAY DIFFRACTIONr_scangle_it6.346114523
Refine LS restraints NCS

Ens-ID: 1 / Number: 4428 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1ALOOSE POSITIONAL0.275
2BLOOSE POSITIONAL0.325
3CLOOSE POSITIONAL0.35
4DLOOSE POSITIONAL0.285
1ALOOSE THERMAL2.7610
2BLOOSE THERMAL2.5710
3CLOOSE THERMAL2.2610
4DLOOSE THERMAL2.7310
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.285 529 -
Rwork0.238 10120 -
all-10649 -
obs--69.53 %

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