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- PDB-4e6m: Crystal structure of Putative dehydratase protein from Salmonella... -

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Entry
Database: PDB / ID: 4e6m
TitleCrystal structure of Putative dehydratase protein from Salmonella enterica subsp. enterica serovar Typhimurium (Salmonella typhimurium)
ComponentsPutative dehydratase protein
KeywordsStructural Genomics / Unknown Function / PROTEIN STRUCTURE INITIATIVE / NEW YORK STRUCTURAL GENOMICS RESEARCH CONSORTIUM / NYSGRC / PSI-Biology
Function / homology
Function and homology information


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 ...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
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsMalashkevich, V.N. / Bhosle, R. / Toro, R. / Hillerich, B. / Gizzi, A. / Garforth, S. / Kar, A. / Chan, M.K. / Lafluer, J. / Patel, H. ...Malashkevich, V.N. / Bhosle, R. / Toro, R. / Hillerich, B. / Gizzi, A. / Garforth, S. / Kar, A. / Chan, M.K. / Lafluer, J. / Patel, H. / Matikainen, B. / Chamala, S. / Lim, S. / Celikgil, A. / Villegas, G. / Evans, B. / Zenchek, W. / Love, J. / Fiser, A. / Khafizov, K. / Seidel, R. / Bonanno, J.B. / Almo, S.C. / New York Structural Genomics Research Consortium (NYSGRC)
CitationJournal: To be Published
Title: Crystal structure of Putative dehydratase protein from Salmonella enterica subsp. enterica serovar Typhimurium (Salmonella typhimurium)
Authors: Malashkevich, V.N. / Bhosle, R. / Toro, R. / Hillerich, B. / Gizzi, A. / Garforth, S. / Kar, A. / Chan, M.K. / Lafluer, J. / Patel, H. / Matikainen, B. / Chamala, S. / Lim, S. / Celikgil, A. ...Authors: Malashkevich, V.N. / Bhosle, R. / Toro, R. / Hillerich, B. / Gizzi, A. / Garforth, S. / Kar, A. / Chan, M.K. / Lafluer, J. / Patel, H. / Matikainen, B. / Chamala, S. / Lim, S. / Celikgil, A. / Villegas, G. / Evans, B. / Zenchek, W. / Love, J. / Fiser, A. / Khafizov, K. / Seidel, R. / Bonanno, J.B. / Almo, S.C.
History
DepositionMar 15, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 4, 2012Provider: repository / Type: Initial release
Revision 1.1May 9, 2012Group: Structure summary
Revision 1.2Sep 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_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_asym_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_asym_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

Downloads & links

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Assembly

Deposited unit
A: Putative dehydratase protein
B: Putative dehydratase protein
C: Putative dehydratase protein
D: Putative dehydratase protein
E: Putative dehydratase protein
F: Putative dehydratase protein
G: Putative dehydratase protein
H: Putative dehydratase protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)380,76634
Polymers377,4838
Non-polymers3,28326
Water42,3532351
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area50610 Å2
ΔGint-257 kcal/mol
Surface area81380 Å2
MethodPISA
2
A: Putative dehydratase protein
B: Putative dehydratase protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,2519
Polymers94,3712
Non-polymers8807
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6530 Å2
ΔGint-54 kcal/mol
Surface area26190 Å2
MethodPISA
3
C: Putative dehydratase protein
D: Putative dehydratase protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,1328
Polymers94,3712
Non-polymers7626
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7100 Å2
ΔGint-58 kcal/mol
Surface area25940 Å2
MethodPISA
4
E: Putative dehydratase protein
F: Putative dehydratase protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,1328
Polymers94,3712
Non-polymers7626
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7170 Å2
ΔGint-59 kcal/mol
Surface area26130 Å2
MethodPISA
5
G: Putative dehydratase protein
H: Putative dehydratase protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,2519
Polymers94,3712
Non-polymers8807
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6920 Å2
ΔGint-53 kcal/mol
Surface area26010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.128, 87.137, 200.586
Angle α, β, γ (deg.)90.000, 91.390, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Putative dehydratase protein /


Mass: 47185.414 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Strain: subsp. enterica serovar Typhimurium / Gene: STM2273 / Plasmid: BC-PSGX3(BC) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)CODON+RIL / References: UniProt: Q8ZNH1
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Chemical
ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2351 / 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: 2.62 Å3/Da / Density % sol: 53.02 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M hepes, pH 7.5, 70% MPD, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 16, 2012
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 332081 / % possible obs: 92.4 % / Redundancy: 2.7 % / Rmerge(I) obs: 0.063 / Χ2: 1.102 / Net I/σ(I): 10.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.8-1.832.40.944163761.158191.6
1.83-1.862.40.784163311.201191.5
1.86-1.92.40.717163431.232191.1
1.9-1.942.40.556162631.254190.9
1.94-1.982.40.411161891.269190.2
1.98-2.032.50.325159831.249189.6
2.03-2.082.50.276159711.283189.3
2.08-2.132.60.237160081.286189
2.13-2.22.60.196157681.207188.4
2.2-2.272.60.171158041.288188.1
2.27-2.352.70.147157901.222187.6
2.35-2.442.70.13158741.19189
2.44-2.552.80.109163701.103191
2.55-2.692.80.092168521.107193.9
2.69-2.862.80.075172450.964196
2.86-3.082.90.065176250.905197.8
3.08-3.3930.051176920.83198.2
3.39-3.8830.038177340.829198.1
3.88-4.8830.03177370.846197.8
4.88-503.10.027181261.085198.3

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å46.25 Å
Translation2.5 Å46.25 Å

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASER2.3.0phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
CBASSdata collection
HKL-3000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2GL5

2gl5


Resolution: 1.8→19.96 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.957 / WRfactor Rfree: 0.2029 / WRfactor Rwork: 0.1717 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8258 / SU B: 5.561 / SU ML: 0.084 / SU R Cruickshank DPI: 0.1211 / SU Rfree: 0.1156 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.121 / ESU R Free: 0.116 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2059 16680 5 %RANDOM
Rwork0.1731 ---
obs0.1748 331066 91.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 101.74 Å2 / Biso mean: 27.9497 Å2 / Biso min: 14.61 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.8→19.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25072 0 208 2351 27631
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0226153
X-RAY DIFFRACTIONr_angle_refined_deg1.3561.96735512
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.56753313
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.70224.5081209
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.085154477
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2215144
X-RAY DIFFRACTIONr_chiral_restr0.0930.23903
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02119864
LS refinement shellResolution: 1.8→1.846 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.344 1120 -
Rwork0.31 21770 -
all-22890 -
obs--87.71 %
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)
10.3985-0.0409-0.03280.2176-0.01760.56250.0140.04340.09490.0284-0.0198-0.0581-0.09830.14160.00570.058-0.02850.00850.04330.01250.082681.402917.761945.6207
20.35580.03360.06060.2397-0.0930.47570.0155-0.0311-0.1157-0.0227-0.0325-0.070.08150.11840.0170.06510.0302-0.00240.03850.01350.108580.9766-13.783955.8446
30.39430.0444-0.06660.2566-0.10080.5690.034-0.04240.05910.01980.02370.0461-0.1277-0.1887-0.05770.04640.04370.02930.0760.020.059519.377512.140962.7197
40.4198-0.00780.01430.2013-0.03620.55890.01470.0748-0.0788-0.00840.01330.05020.0819-0.1756-0.0280.0209-0.0264-0.01970.07190.00140.052519.8369-7.305636.024
50.53680.00540.09430.1482-0.04230.32280.0050.12630.1407-0.01030.0138-0.0115-0.1017-0.0605-0.01880.10290.02850.01350.05350.05240.085241.398224.338724.6021
60.58990.0262-0.02740.2802-0.08860.33760.01720.1902-0.0663-0.0488-0.0049-0.01070.04060.0269-0.01230.06720.01360.01290.0654-0.02220.013460.9045-1.038916.9394
70.6599-0.05930.00790.2872-0.08210.36180.0183-0.18510.04340.0613-0.0072-0.0119-0.04010.0185-0.01120.0702-0.0097-0.00630.0546-0.01270.00659.46995.276183.5938
80.59450.0315-0.07880.1464-0.00380.39220.0028-0.1272-0.1660.01090.0083-0.00770.0895-0.0548-0.01120.1038-0.01420.00240.04550.05570.103739.9591-19.76775.0433
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 503
2X-RAY DIFFRACTION2B0 - 703
3X-RAY DIFFRACTION3C0 - 503
4X-RAY DIFFRACTION4D0 - 503
5X-RAY DIFFRACTION5E0 - 503
6X-RAY DIFFRACTION6F0 - 701
7X-RAY DIFFRACTION7G0 - 503
8X-RAY DIFFRACTION8H0 - 504

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