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- PDB-3s7z: Crystal Structure of Putative Aspartate Racemase from Salmonella ... -

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Basic information

Entry
Database: PDB / ID: 3s7z
TitleCrystal Structure of Putative Aspartate Racemase from Salmonella Typhimurium Complexed with Succinate
ComponentsPutative aspartate racemase
KeywordsISOMERASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / alpha beta fold / racemase / cytosol
Function / homology
Function and homology information


amino-acid racemase activity / metal ion binding
Similarity search - Function
Aspartate racemase / Asp/Glu racemase, active site 1 / Aspartate and glutamate racemases signature 1. / Asp/Glu racemase, active site 2 / Aspartate and glutamate racemases signature 2. / Rossmann fold - #1860 / Asp/Glu racemase / Asp/Glu/hydantoin racemase / Asp/Glu/Hydantoin racemase / Rossmann fold ...Aspartate racemase / Asp/Glu racemase, active site 1 / Aspartate and glutamate racemases signature 1. / Asp/Glu racemase, active site 2 / Aspartate and glutamate racemases signature 2. / Rossmann fold - #1860 / Asp/Glu racemase / Asp/Glu/hydantoin racemase / Asp/Glu/Hydantoin racemase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
sucrose / SUCCINIC ACID / Aspartate racemase
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.002 Å
AuthorsMaltseva, N. / Zhang, R. / Kwon, K. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: Crystal Structure of Putative Aspartate Racemase from Salmonella Typhimurium Complexed with Succinate.
Authors: Maltseva, N. / Zhang, R. / Kwon, K. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionMay 27, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 5, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.name
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_asym.entity_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative aspartate racemase
B: Putative aspartate racemase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,6966
Polymers59,0932
Non-polymers6034
Water5,278293
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3750 Å2
ΔGint-22 kcal/mol
Surface area18370 Å2
MethodPISA
2
B: Putative aspartate racemase
hetero molecules

A: Putative aspartate racemase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,6966
Polymers59,0932
Non-polymers6034
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555y,-x+y,z+1/61
Buried area2160 Å2
ΔGint-13 kcal/mol
Surface area19960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.826, 84.826, 114.127
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Putative aspartate racemase


Mass: 29546.578 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Strain: LT2 / Gene: STM4510 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 magic / References: UniProt: Q8ZJZ9
#2: Polysaccharide beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose / sucrose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: sucrose
DescriptorTypeProgram
DFrufb2-1DGlcpaGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[ha122h-2b_2-5][a2122h-1a_1-5]/1-2/a2-b1WURCSPDB2Glycan 1.1.0
[][b-D-Fruf]{[(2+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#3: Chemical ChemComp-SIN / SUCCINIC ACID


Mass: 118.088 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O4
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 293 / 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: 2.01 Å3/Da / Density % sol: 38.68 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.8M succinic acid, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97935 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 17, 2009 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97935 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 31375 / Num. obs: 31375 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.3 % / Biso Wilson estimate: 17.42 Å2 / Rsym value: 0.155 / Net I/σ(I): 7.2
Reflection shellResolution: 2→2.03 Å / Redundancy: 11.4 % / Mean I/σ(I) obs: 5.5 / Num. unique all: 1542 / Rsym value: 0.699 / % possible all: 100

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000data collection
HKL-3000phasing
SHELXmodel building
RESOLVEmodel building
BUCCANEERmodel building
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-3000data reduction
HKL-3000data scaling
SHELXphasing
RESOLVEphasing
BUCCANEERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.002→45.065 Å / SU ML: 0.45 / Isotropic thermal model: mixed / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 17.47 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.185 1576 5.05 %random
Rwork0.148 ---
all0.15 31201 --
obs0.15 31201 99.59 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.05 Å2 / ksol: 0.391 e/Å3
Displacement parametersBiso mean: 21 Å2
Baniso -1Baniso -2Baniso -3
1-2.795 Å20 Å2-0 Å2
2--2.795 Å2-0 Å2
3----5.5899 Å2
Refinement stepCycle: LAST / Resolution: 2.002→45.065 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3532 0 40 293 3865
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083946
X-RAY DIFFRACTIONf_angle_d1.2815416
X-RAY DIFFRACTIONf_dihedral_angle_d12.8481494
X-RAY DIFFRACTIONf_chiral_restr0.093630
X-RAY DIFFRACTIONf_plane_restr0.007712
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2.0021-2.06670.22991400.15972681282198
2.0667-2.14060.22791260.16152623274999
2.1406-2.22630.17441440.15392700284499
2.2263-2.32760.20631400.144626862826100
2.3276-2.45030.21031440.146826932837100
2.4503-2.60380.1811670.151826502817100
2.6038-2.80480.19441370.154327102847100
2.8048-3.0870.21911360.166627162852100
3.087-3.53360.19261380.153527212859100
3.5336-4.45130.15691430.128427222865100
4.4513-45.07640.15271610.138827232884100
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)
16.2793.1444-3.3466.8955-4.14686.6045-0.2830.5141-0.0464-0.6147-0.0233-0.43650.42680.13150.28150.12330.02520.0290.13420.06040.159741.39538.98041.069
20.5162-0.05250.10240.67910.22892.9011-0.01630.02260.0247-0.0008-0.1058-0.0803-0.03520.00710.14520.08150.0085-0.00410.07750.03490.123534.44276.89185.3699
32.4997-0.5687-1.3921.49190.51767.2618-0.029-0.0874-0.01910.0679-0.0454-0.343-0.07890.60360.04780.1042-0.031-0.05250.18940.0540.226548.43636.719210.9461
40.3754-0.3329-0.51431.31580.16181.562-0.08070.05610.1966-0.0415-0.0152-0.2748-0.2850.31260.06440.1452-0.0474-0.03630.16410.0480.160840.222516.96219.6238
51.1438-1.12551.42553.6561-2.86073.1534-0.1769-0.13680.20650.34980.11310.0518-0.6151-0.10350.09290.19910.018-0.01920.1160.00490.135526.071123.867116.6494
61.8797-0.0196-0.3993.4208-0.58522.5047-0.0181-0.1631-0.04310.19520.02240.2416-0.0947-0.29-0.01710.0967-0.00050.0080.1510.02410.117819.113912.391319.7946
70.9832-0.2750.12372.3509-0.40662.8424-0.19330.10830.0501-0.0395-0.02520.0909-0.016-0.26790.2150.09270.0099-0.04280.11330.0070.116426.798614.40163.7846
82.2535-0.93771.71124.8556-2.04918.5036-0.2553-0.12860.08950.5847-0.1768-0.5734-0.22250.85590.4160.11470.0259-0.01870.20420.06510.172644.1467-5.80794.6576
90.4120.24970.06120.8218-0.02851.0856-0.01730.0309-0.0929-0.0476-0.0372-0.16450.14270.17280.05410.09860.0430.0390.12690.04170.145836.7283-10.7204-6.735
100.8506-0.08910.50391.1199-0.46182.0816-0.0628-0.08980.0111-0.03470.06340.1260.0447-0.3830.01120.09710.00740.04220.13520.0260.134523.8133-10.1247-7.1943
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 0:12)
2X-RAY DIFFRACTION2chain 'A' and (resseq 13:60)
3X-RAY DIFFRACTION3chain 'A' and (resseq 61:74)
4X-RAY DIFFRACTION4chain 'A' and (resseq 75:111)
5X-RAY DIFFRACTION5chain 'A' and (resseq 112:140)
6X-RAY DIFFRACTION6chain 'A' and (resseq 141:191)
7X-RAY DIFFRACTION7chain 'A' and (resseq 192:232)
8X-RAY DIFFRACTION8chain 'B' and (resseq -2:12)
9X-RAY DIFFRACTION9chain 'B' and (resseq 13:148)
10X-RAY DIFFRACTION10chain 'B' and (resseq 149:232)

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