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- PDB-2rfl: Crystal structure of the putative phosphohistidine phosphatase Si... -

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Basic information

Entry
Database: PDB / ID: 2rfl
TitleCrystal structure of the putative phosphohistidine phosphatase SixA from Agrobacterium tumefaciens
ComponentsPutative phosphohistidine phosphatase SixA
KeywordsHYDROLASE / ISOMERASE / alpha-beta-alpha sandwich / Structural Genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


Phosphoglycerate mutase family / Phosphoglycerate mutase-like / Histidine phosphatase superfamily, clade-1 / Histidine phosphatase superfamily (branch 1) / Histidine phosphatase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETIC ACID / THIOCYANATE ION / Uncharacterized protein / :
Similarity search - Component
Biological speciesAgrobacterium tumefaciens str. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.35 Å
AuthorsKim, Y. / Binkowski, T. / Xu, X. / Edwards, A.M. / Savchenko, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal Structure of the Putative Phosphohistidine Phosphatase SixA from Agrobacterium tumefaciens.
Authors: Kim, Y. / Binkowski, T. / Xu, X. / Gu, J. / Que, Q. / Savchenko, A. / Edwards, A.M. / Joachimiak, A.
History
DepositionOct 1, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 23, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative phosphohistidine phosphatase SixA
B: Putative phosphohistidine phosphatase SixA
C: Putative phosphohistidine phosphatase SixA
D: Putative phosphohistidine phosphatase SixA
E: Putative phosphohistidine phosphatase SixA
F: Putative phosphohistidine phosphatase SixA
G: Putative phosphohistidine phosphatase SixA
H: Putative phosphohistidine phosphatase SixA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)153,76412
Polymers153,4628
Non-polymers3024
Water10,467581
1
A: Putative phosphohistidine phosphatase SixA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,3333
Polymers19,1831
Non-polymers1502
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Putative phosphohistidine phosphatase SixA


Theoretical massNumber of molelcules
Total (without water)19,1831
Polymers19,1831
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Putative phosphohistidine phosphatase SixA


Theoretical massNumber of molelcules
Total (without water)19,1831
Polymers19,1831
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Putative phosphohistidine phosphatase SixA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,2432
Polymers19,1831
Non-polymers601
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Putative phosphohistidine phosphatase SixA


Theoretical massNumber of molelcules
Total (without water)19,1831
Polymers19,1831
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: Putative phosphohistidine phosphatase SixA


Theoretical massNumber of molelcules
Total (without water)19,1831
Polymers19,1831
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
G: Putative phosphohistidine phosphatase SixA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,2752
Polymers19,1831
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
8
H: Putative phosphohistidine phosphatase SixA


Theoretical massNumber of molelcules
Total (without water)19,1831
Polymers19,1831
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.966, 201.503, 72.717
Angle α, β, γ (deg.)90.00, 113.98, 90.00
Int Tables number4
Space group name H-MP1211
DetailsAuthors state that the biological unit is unknown.

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Components

#1: Protein
Putative phosphohistidine phosphatase SixA / AGR_C_2511p / Uncharacterized protein Atu1358 / Phosphoglycerate mutase


Mass: 19182.713 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrobacterium tumefaciens str. (bacteria)
Species: Agrobacterium tumefaciens / Strain: C58 / Gene: AGR_C_2511, Atu1358 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q8UFN9, UniProt: A9CJ67*PLUS, EC: 5.4.2.1, EC: 3.1.3.13, bisphosphoglycerate mutase
#2: Chemical ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CNS
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 581 / 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: 2.57 Å3/Da / Density % sol: 52.18 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.2 M Thiocyanate, 20 % PEG 3350, 2 % Sucrose, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9796 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 17, 2007 / Details: mirrors
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 2.35→50 Å / Num. all: 63011 / Num. obs: 63011 / % possible obs: 97.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 40.75 Å2 / Rsym value: 0.116 / Net I/σ(I): 10.1
Reflection shellResolution: 2.35→2.43 Å / Redundancy: 2.1 % / Mean I/σ(I) obs: 1.8 / Num. unique all: 5485 / Rsym value: 0.422 / % possible all: 85.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
SBC-Collectdata collection
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
HKL-3000phasing
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.35→47.25 Å / Cor.coef. Fo:Fc: 0.911 / Cor.coef. Fo:Fc free: 0.878 / SU B: 18.734 / SU ML: 0.219 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.298
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: Program CCI has also been used in refinement
RfactorNum. reflection% reflectionSelection details
Rfree0.283 6323 10.1 %RANDOM
Rwork0.23 ---
all0.236 56318 --
obs0.236 56318 97.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 45.693 Å2
Baniso -1Baniso -2Baniso -3
1--1.02 Å20 Å2-0.83 Å2
2--1.78 Å20 Å2
3----1.43 Å2
Refinement stepCycle: LAST / Resolution: 2.35→47.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9516 0 19 581 10116
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0229987
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8061.95213584
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.92851240
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.14322.972498
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.715151594
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.92415107
X-RAY DIFFRACTIONr_chiral_restr0.1250.21513
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.027763
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2660.25085
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3190.26476
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.240.2604
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3440.274
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3270.210
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.0371.56198
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.12129912
X-RAY DIFFRACTIONr_scbond_it4.21633789
X-RAY DIFFRACTIONr_scangle_it6.3654.53672
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.35→2.411 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 409 -
Rwork0.253 3581 -
obs-3990 84.97 %
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)
11.01520.25520.4121.26760.48780.28990.02640.1365-0.02640.0677-0.0822-0.0469-0.0038-0.07550.0558-0.2101-0.0166-0.0116-0.20670.0071-0.2597-37.667910.5614-8.6706
20.2101-0.50240.08661.2048-0.17970.25930.0579-0.0262-0.0222-0.0366-0.07760.0170.13030.0360.0197-0.25440.00570.0125-0.1443-0.0191-0.2292-15.3454-5.8778-1.9356
30.5405-0.1101-0.26191.2458-0.7751.34950.0127-0.0458-0.06960.0943-0.11610.0374-0.07840.03080.1034-0.30150.0045-0.0083-0.1992-0.0274-0.2794-15.26261.470825.2282
41.11940.2774-0.18770.1818-0.13030.0936-0.00270.1121-0.0742-0.02470.0168-0.04390.08740.0848-0.0141-0.18630.02130.0212-0.151-0.0215-0.2631-17.925462.6377-4.9178
50.5178-0.06510.10420.5745-0.69121.4601-0.00120.0223-0.1496-0.05960.00620.05290.1278-0.196-0.0051-0.3035-0.00140.0098-0.2838-0.0215-0.2652-40.86589.072621.1785
61.856-0.33090.39130.3096-0.32971.32010.0089-0.2107-0.10760.06580.01610.04710.09070.0267-0.025-0.28250.01640.0027-0.2246-0.0021-0.2625-18.3732-6.923628.2886
70.6527-0.1092-0.46250.92950.10620.6451-0.04580.17390.025-0.03840.0072-0.0443-0.0357-0.04750.0387-0.31910.00420.0025-0.26850.0022-0.32-40.547946.52361.9153
80.61920.0217-0.27590.54820.13170.15940.1207-0.0370.0603-0.1042-0.10670.0048-0.02780.0406-0.014-0.18860.02680.0204-0.1647-0.0119-0.2524-37.717545.156131.6642
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA4 - 1676 - 169
2X-RAY DIFFRACTION2BB5 - 1677 - 169
3X-RAY DIFFRACTION3CC5 - 1677 - 169
4X-RAY DIFFRACTION4DD4 - 1686 - 170
5X-RAY DIFFRACTION5EE5 - 1687 - 170
6X-RAY DIFFRACTION6FF4 - 1666 - 168
7X-RAY DIFFRACTION7GG4 - 1676 - 169
8X-RAY DIFFRACTION8HH3 - 1675 - 169

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