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- PDB-2ooc: Crystal structure of Histidine Phosphotransferase ShpA (NP_419930... -

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Basic information

Entry
Database: PDB / ID: 2ooc
TitleCrystal structure of Histidine Phosphotransferase ShpA (NP_419930.1) from Caulobacter crescentus at 1.52 A resolution
ComponentsHistidine phosphotransferase
KeywordsTRANSFERASE / NP_419930.1 / hypothetical protein / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


phosphorelay signal transduction system / transferase activity
Similarity search - Function
HPT domain / Hpt domain / Signal transduction histidine kinase, phosphotransfer (Hpt) domain / HPT domain superfamily / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Histidine phosphotransferase / Histidine phosphotransferase
Similarity search - Component
Biological speciesCaulobacter crescentus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.52 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Crystal structure of histidine phosphotransfer protein ShpA, an essential regulator of stalk biogenesis in Caulobacter crescentus.
Authors: Xu, Q. / Carlton, D. / Miller, M.D. / Elsliger, M.A. / Krishna, S.S. / Abdubek, P. / Astakhova, T. / Burra, P. / Chiu, H.J. / Clayton, T. / Deller, M.C. / Duan, L. / Elias, Y. / Feuerhelm, J. ...Authors: Xu, Q. / Carlton, D. / Miller, M.D. / Elsliger, M.A. / Krishna, S.S. / Abdubek, P. / Astakhova, T. / Burra, P. / Chiu, H.J. / Clayton, T. / Deller, M.C. / Duan, L. / Elias, Y. / Feuerhelm, J. / Grant, J.C. / Grzechnik, A. / Grzechnik, S.K. / Han, G.W. / Jaroszewski, L. / Jin, K.K. / Klock, H.E. / Knuth, M.W. / Kozbial, P. / Kumar, A. / Marciano, D. / McMullan, D. / Morse, A.T. / Nigoghossian, E. / Okach, L. / Oommachen, S. / Paulsen, J. / Reyes, R. / Rife, C.L. / Sefcovic, N. / Trame, C. / Trout, C.V. / van den Bedem, H. / Weekes, D. / Hodgson, K.O. / Wooley, J. / Deacon, A.M. / Godzik, A. / Lesley, S.A. / Wilson, I.A.
History
DepositionJan 25, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 6, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Jan 25, 2023Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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 / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999 SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ... SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE, FOLLOWED BY THE TARGET SEQUENCE.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Histidine phosphotransferase
B: Histidine phosphotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9257
Polymers24,1592
Non-polymers7675
Water3,945219
1
A: Histidine phosphotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,3663
Polymers12,0791
Non-polymers2862
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Histidine phosphotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,5604
Polymers12,0791
Non-polymers4813
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.373, 62.373, 115.574
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg label comp-ID: GLY / Refine code: 6

Dom-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1LYSAA8 - 1119 - 112
2GLYBB8 - 1129 - 113

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Components

#1: Protein Histidine phosphotransferase


Mass: 12079.277 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caulobacter crescentus (bacteria) / Species: Caulobacter vibrioides / Strain: CB15 / Gene: NP_419930.1, shpA, CC1114 / Plasmid: speedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100
References: UniProt: A0EJF9, UniProt: Q9A980*PLUS, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with a nitrogenous group as acceptor
#2: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 219 / 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: 2

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)Description
12.6954.2THE STRUCTURE WAS SOLVED BY MAD METHOD USING A DIFFERENT CRYSTAL. THE PHASE RESTRAINTS FROM THAT CRYSTAL WERE USED IN THE CURRENT REFINEMENT.
2THE STRUCTURE WAS SOLVED BY MAD METHOD USING A DIFFERENT CRYSTAL. THE PHASE RESTRAINTS FROM THAT CRYSTAL WERE USED IN THE CURRENT REFINEMENT.
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2771vapor diffusion, sitting drop6.9NANODROP, 1.5% polyethylene glycol 400, 15.0% Glycerol, 1.9M ammonium sulfate, 0.1M HEPES pH 6.9, VAPOR DIFFUSION, SITTING DROP, temperature 277K
2772vapor diffusion, sitting drop6.9NANODROP, 1.5% polyethylene glycol 400, 15.0% Glycerol, 1.9M ammonium sulfate, 0.1M HEPES pH 6.9, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21002
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSSRL BL11-110.91837
SYNCHROTRONSSRL BL1-520.918381, 0.978575
Detector
TypeIDDetectorDateDetails
MARMOSAIC 325 mm CCD1CCDJan 18, 2007Flat mirror (vertical focusing)
ADSC QUANTUM 42CCDJan 17, 20071m long Rh coated bent cylindrical mirror for horizontal and vertical focussing
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-IDMonochromator
1SINGLE WAVELENGTHMx-ray1
2MADMx-ray1Double-crystal
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.9183811
30.9785751
ReflectionResolution: 1.52→28.89 Å / Num. obs: 40951 / % possible obs: 100 % / Redundancy: 6.9 % / Biso Wilson estimate: 23.88 Å2 / Rmerge(I) obs: 0.068 / Rsym value: 0.068 / Net I/σ(I): 6.2
Reflection shell

Diffraction-ID: 1,2

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.52-1.565.10.8110.91527529930.811100
1.56-1.65.20.6491.21495928950.649100
1.6-1.655.20.5011.51471628230.501100
1.65-1.75.30.38121441527360.381100
1.7-1.765.30.3332.31437726950.333100
1.76-1.825.40.2473.11375425570.247100
1.82-1.895.40.1983.81366025210.198100
1.89-1.965.40.1594.61298924060.159100
1.96-2.055.50.1235.61247422880.123100
2.05-2.155.40.1036.51212222420.103100
2.15-2.276.70.12351418221110.123100
2.27-2.49.40.1285.21893820120.128100
2.4-2.5710.90.10862038818780.108100
2.57-2.7810.90.0877.61920517660.087100
2.78-3.0410.90.079.21784816380.07100
3.04-3.410.70.06110.11597214860.061100
3.4-3.9210.60.05111.21415313290.051100
3.92-4.8110.40.05111.61181911410.051100
4.81-6.89.90.0512.489238970.05100
6.8-28.947.70.04512.541435370.04598.7

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
SHELXphasing
REFMAC5.2.0019refinement
SCALAdata scaling
PDB_EXTRACT2data extraction
MAR345CCDdata collection
MOSFLMdata reduction
CCP4(SCALA)data scaling
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.52→28.89 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.961 / SU B: 3.072 / SU ML: 0.054 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.063 / ESU R Free: 0.069
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3. 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. 4. PG4 AND GOL ARE MODELED BASED ON THE CRYSTALLIZATION CONDITIONS. 5. B21 HAS POORLY DEFINED ELECTRON DENSITY. RESIDUES 0-7 IN BOTH CHAINS (A AND B) ARE DISORDERED.
RfactorNum. reflection% reflectionSelection details
Rfree0.202 2051 5 %RANDOM
Rwork0.166 ---
all0.168 ---
obs0.168 40897 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 22.111 Å2
Baniso -1Baniso -2Baniso -3
1-1.12 Å20.56 Å20 Å2
2--1.12 Å20 Å2
3----1.67 Å2
Refinement stepCycle: LAST / Resolution: 1.52→28.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1547 0 37 219 1803
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0221702
X-RAY DIFFRACTIONr_bond_other_d0.0090.021131
X-RAY DIFFRACTIONr_angle_refined_deg1.7041.9582315
X-RAY DIFFRACTIONr_angle_other_deg1.04732762
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6085232
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.18324.19881
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.71215255
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.3331511
X-RAY DIFFRACTIONr_chiral_restr0.1140.2251
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021965
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02358
X-RAY DIFFRACTIONr_nbd_refined0.230.2400
X-RAY DIFFRACTIONr_nbd_other0.1910.21161
X-RAY DIFFRACTIONr_nbtor_refined0.1880.2859
X-RAY DIFFRACTIONr_nbtor_other0.0920.2856
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1930.2157
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0870.29
X-RAY DIFFRACTIONr_symmetry_vdw_other0.30.232
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2040.211
X-RAY DIFFRACTIONr_mcbond_it2.35231153
X-RAY DIFFRACTIONr_mcbond_other0.5883444
X-RAY DIFFRACTIONr_mcangle_it3.03751682
X-RAY DIFFRACTIONr_scbond_it5.2988694
X-RAY DIFFRACTIONr_scangle_it7.78611620
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 1157 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
LOOSE POSITIONAL1.125
LOOSE THERMAL3.2810
LS refinement shellResolution: 1.52→1.56 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.282 163 -
Rwork0.263 2778 -
obs-2941 98.66 %
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)
11.9888-0.7866-0.61490.46270.57520.9294-0.0353-0.0212-0.0982-0.14440.0697-0.057-0.1103-0.0085-0.0345-0.0259-0.02860.0089-0.0153-0.00360.005934.00927.7910.893
20.89970.1368-0.15921.8964-0.9852.54440.0047-0.18550.03890.16810.15120.0902-0.1974-0.2762-0.1559-0.06830.02690.01350.027-0.00230.016341.05537.62820.604
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA8 - 1119 - 112
22BB8 - 1129 - 113

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