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- PDB-3v4b: Crystal structure of an enolase from the soil bacterium Cellvibri... -

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Basic information

Entry
Database: PDB / ID: 3v4b
TitleCrystal structure of an enolase from the soil bacterium Cellvibrio japonicus (TARGET EFI-502161) with bound MG and L-tartrate
ComponentsStarvation sensing protein rspA
KeywordsLYASE / Enolase / enzyme function initiative / EFI / Structural Genomics
Function / homology
Function and homology information


mannonate dehydratase / mannonate dehydratase activity / Lyases; Carbon-oxygen lyases; Hydro-lyases / amino acid catabolic process / carbohydrate catabolic process / magnesium ion binding
Similarity search - Function
D-mannonate dehydratase-like / Mandelate racemase / muconate lactonizing enzyme family signature 1. / Mandelate racemase/muconate lactonizing enzyme, conserved site / Mandelate racemase DgoD-like / Mandelate racemase/muconate lactonizing enzyme, N-terminal domain / Mandelate racemase / muconate lactonizing enzyme, N-terminal domain / Mandelate racemase/muconate lactonizing enzyme, C-terminal / Mandelate racemase / muconate lactonizing enzyme, C-terminal domain / Enolase C-terminal domain-like / Enolase C-terminal domain-like ...D-mannonate dehydratase-like / Mandelate racemase / muconate lactonizing enzyme family signature 1. / Mandelate racemase/muconate lactonizing enzyme, conserved site / Mandelate racemase DgoD-like / Mandelate racemase/muconate lactonizing enzyme, N-terminal domain / Mandelate racemase / muconate lactonizing enzyme, N-terminal domain / Mandelate racemase/muconate lactonizing enzyme, C-terminal / Mandelate racemase / muconate lactonizing enzyme, C-terminal domain / Enolase C-terminal domain-like / Enolase C-terminal domain-like / Enolase-like C-terminal domain / Enolase-like, N-terminal domain / Enolase-like, N-terminal / Enolase-like, C-terminal domain superfamily / Enolase-like; domain 1 / TIM Barrel / Alpha-Beta Barrel / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
L(+)-TARTARIC ACID / D-galactonate dehydratase family member RspA
Similarity search - Component
Biological speciesCellvibrio japonicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsVetting, M.W. / Toro, R. / Bhosle, R. / Wasserman, S.R. / Morisco, L.L. / Sojitra, S. / Seidel, R.D. / Hillerich, B. / Washington, E. / Scott Glenn, A. ...Vetting, M.W. / Toro, R. / Bhosle, R. / Wasserman, S.R. / Morisco, L.L. / Sojitra, S. / Seidel, R.D. / Hillerich, B. / Washington, E. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hammonds, J. / Al Obaidi, N. / Zencheck, W.D. / Imker, H.J. / Gerlt, J.A. / Almo, S.C. / Enzyme Function Initiative (EFI)
CitationJournal: to be published
Title: Crystal structure of an enolase from the soil bacterium Cellvibrio japonicus (TARGET EFI-502161) with bound MG and l-tartrate
Authors: Vetting, M.W. / Toro, R. / Bhosle, R. / Wasserman, S.R. / Morisco, L.L. / Sojitra, S. / Seidel, R.D. / Hillerich, B. / Washington, E. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / ...Authors: Vetting, M.W. / Toro, R. / Bhosle, R. / Wasserman, S.R. / Morisco, L.L. / Sojitra, S. / Seidel, R.D. / Hillerich, B. / Washington, E. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hammonds, J. / Obaidi, N. / Zencheck, W.D. / Imker, H.J. / Gerlt, J.A. / Almo, S.C.
History
DepositionDec 14, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 28, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_alt_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_alt_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.pdbx_ptnr2_label_alt_id / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Starvation sensing protein rspA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,2314
Polymers48,0211
Non-polymers2103
Water8,557475
1
A: Starvation sensing protein rspA
hetero molecules
x 8


Theoretical massNumber of molelcules
Total (without water)385,85032
Polymers384,1728
Non-polymers1,67924
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
crystal symmetry operation5_555-x,y,-z1
crystal symmetry operation6_555x,-y,-z1
crystal symmetry operation7_555y,x,-z1
crystal symmetry operation8_555-y,-x,-z1
Buried area50110 Å2
ΔGint-211 kcal/mol
Surface area81600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.715, 124.715, 110.871
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11A-507-

CL

21A-525-

HOH

31A-544-

HOH

41A-557-

HOH

51A-704-

HOH

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Components

#1: Protein Starvation sensing protein rspA


Mass: 48021.453 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cellvibrio japonicus (bacteria) / Strain: Ueda107 / Gene: rspA, CJA_3069 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B3PDB1
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-TLA / L(+)-TARTARIC ACID / Tartaric acid


Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O6
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 475 / 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: 2.24 Å3/Da / Density % sol: 45.2 %
Crystal growTemperature: 298 K / Method: sitting drop vapor diffusion / pH: 4.6
Details: Protein (10 mM Hepes, pH 7.8, 150 mM NaCl, 10% glycerol, 5 mM DTT, 5 mM MgCl2; Reservoir (0.2M KNaTartrate, 20% Peg3350); Cryoprotection (20% glycerol), sitting drop vapor diffusion, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9793 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Nov 15, 2011 / Details: MIRRORS
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.4→88.187 Å / Num. all: 85453 / Num. obs: 85453 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13.9 % / Biso Wilson estimate: 10.8 Å2 / Rmerge(I) obs: 0.071 / Rsym value: 0.071 / Net I/σ(I): 25.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.4-1.4812.60.6231.3156024123540.623100
1.48-1.5713.20.4111.9154066116750.411100
1.57-1.6713.80.2762.8151543110140.276100
1.67-1.8114.30.1973.9146532102620.197100
1.81-1.9814.60.1236.213864794740.123100
1.98-2.2114.70.089.412609885980.08100
2.21-2.5614.60.05912.411085875970.059100
2.56-3.1314.50.04415.49388264710.044100
3.13-4.4314.30.0321.57271950840.03100
4.43-88.18713.70.02326.14000429240.02399.9

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Processing

Software
NameVersionClassificationNB
SCALA3.3.16data scaling
PHENIX1.7.3_928refinement
PDB_EXTRACT3.1data extraction
MAR345dtbdata collection
MOSFLMdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2QJM

2qjm


Resolution: 1.4→32.136 Å / Occupancy max: 1 / Occupancy min: 0.15 / FOM work R set: 0.9135 / SU ML: 0.15 / σ(F): 1.34 / Phase error: 14.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1618 4276 5 %Random
Rwork0.1486 ---
obs0.1493 85437 99.99 %-
all-85437 --
Solvent computationShrinkage radii: 1.24 Å / VDW probe radii: 1.4 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.004 Å2 / ksol: 0.357 e/Å3
Displacement parametersBiso max: 50.5 Å2 / Biso mean: 15.0059 Å2 / Biso min: 4.68 Å2
Baniso -1Baniso -2Baniso -3
1-0.4182 Å20 Å2-0 Å2
2--0.4182 Å2-0 Å2
3----0.8363 Å2
Refinement stepCycle: LAST / Resolution: 1.4→32.136 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3076 0 12 475 3563
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0173301
X-RAY DIFFRACTIONf_angle_d1.6284510
X-RAY DIFFRACTIONf_chiral_restr0.11479
X-RAY DIFFRACTIONf_plane_restr0.01588
X-RAY DIFFRACTIONf_dihedral_angle_d13.8211203
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.4-1.41590.30651500.234826692819
1.4159-1.43260.25681180.224327062824
1.4326-1.450.2191220.199526922814
1.45-1.46840.23421360.182426812817
1.4684-1.48770.20041350.16426632798
1.4877-1.50810.16421490.171826962845
1.5081-1.52970.20471380.161326752813
1.5297-1.55250.18921370.161526582795
1.5525-1.57670.16471430.155127012844
1.5767-1.60260.19221540.150626712825
1.6026-1.63020.18751250.150126852810
1.6302-1.65990.15141270.143226892816
1.6599-1.69180.17861490.144426672816
1.6918-1.72630.1811560.142626862842
1.7263-1.76390.16641490.140326932842
1.7639-1.80490.15151390.140926802819
1.8049-1.850.16071380.143827062844
1.85-1.90.18221340.144726992833
1.9-1.95590.16081350.144127042839
1.9559-2.01910.1631660.147726692835
2.0191-2.09120.1661270.143527182845
2.0912-2.17490.14841610.139626982859
2.1749-2.27390.15541530.136827002853
2.2739-2.39370.1551540.139526892843
2.3937-2.54360.14481590.146827312890
2.5436-2.73990.18151380.147427342872
2.7399-3.01550.12571480.147427202868
3.0155-3.45140.15111340.139927792913
3.4514-4.34670.14061550.133327832938
4.3467-32.14410.15341470.158529193066
Refinement TLS params.Method: refined / Origin x: 10.0344 Å / Origin y: -30.0376 Å / Origin z: 13.9583 Å
111213212223313233
T0.0895 Å20.0078 Å2-0.0182 Å2-0.0607 Å20.0232 Å2--0.0705 Å2
L0.4864 °2-0.2002 °2-0.116 °2-0.5905 °20.1775 °2--0.4789 °2
S-0.0089 Å °-0.0528 Å °-0.0962 Å °0.0434 Å °0.0147 Å °0.0193 Å °0.1324 Å °0.0052 Å °-0.006 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 402
2X-RAY DIFFRACTION1allA1 - 403
3X-RAY DIFFRACTION1allA1 - 880
4X-RAY DIFFRACTION1allA507
5X-RAY DIFFRACTION1allA1 - 404

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