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- PDB-1vr0: Crystal structure of putative 2-phosphosulfolactate phosphatase (... -

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Basic information

Entry
Database: PDB / ID: 1vr0
TitleCrystal structure of putative 2-phosphosulfolactate phosphatase (15026306) from Clostridium acetobutylicum at 2.6 A resolution
ComponentsProbable 2-phosphosulfolactate phosphatase
KeywordsHYDROLASE / 15026306 / putative 2-phosphosulfolactate phosphatase / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI
Function / homology
Function and homology information


2-phosphosulfolactate phosphatase / 2-phosphosulfolactate phosphatase activity / magnesium ion binding
Similarity search - Function
putative 2-phosphosulfolactate phosphatase / ComB-like / ComB-like / ComB-like superfamily / 2-phosphosulpholactate phosphatase / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
(2R)-3-SULFOLACTIC ACID / Probable 2-phosphosulfolactate phosphatase
Similarity search - Component
Biological speciesClostridium acetobutylicum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.49 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: Proteins / Year: 2006
Title: Crystal structure of 2-phosphosulfolactate phosphatase (ComB) from Clostridium acetobutylicum at 2.6 A resolution reveals a new fold with a novel active site.
Authors: DiDonato, M. / Krishna, S.S. / Schwarzenbacher, R. / McMullan, D. / Agarwalla, S. / Brittain, S.M. / Miller, M.D. / Abdubek, P. / Ambing, E. / Axelrod, H.L. / Canaves, J.M. / Chiu, H.J. / ...Authors: DiDonato, M. / Krishna, S.S. / Schwarzenbacher, R. / McMullan, D. / Agarwalla, S. / Brittain, S.M. / Miller, M.D. / Abdubek, P. / Ambing, E. / Axelrod, H.L. / Canaves, J.M. / Chiu, H.J. / Deacon, A.M. / Duan, L. / Elsliger, M.A. / Godzik, A. / Grzechnik, S.K. / Hale, J. / Hampton, E. / Haugen, J. / Jaroszewski, L. / Jin, K.K. / Klock, H.E. / Knuth, M.W. / Koesema, E. / Kreusch, A. / Kuhn, P. / Lesley, S.A. / Levin, I. / Morse, A.T. / Nigoghossian, E. / Okach, L. / Oommachen, S. / Paulsen, J. / Quijano, K. / Reyes, R. / Rife, C.L. / Spraggon, G. / Stevens, R.C. / van den Bedem, H. / White, A. / Wolf, G. / Xu, Q. / Hodgson, K.O. / Wooley, J. / Wilson, I.A.
History
DepositionJan 26, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 15, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.3Oct 25, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.4Jan 25, 2023Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / 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_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_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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 300BIOMOLECULE: 1, 2 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 3 ...BIOMOLECULE: 1, 2 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 3 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). THE AUTHORS STATE THAT SIZE EXCLUSION CHROMATOGRAPHY (SEC) AND STATIC LIGHT SCATTERING SUPPORT THE ASSIGNMENT OF THE BIOLOGICAL OLIGOMERIZATION STATE AS A DIMER.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Probable 2-phosphosulfolactate phosphatase
B: Probable 2-phosphosulfolactate phosphatase
C: Probable 2-phosphosulfolactate phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,6118
Polymers84,0523
Non-polymers5595
Water1,67593
1
A: Probable 2-phosphosulfolactate phosphatase
hetero molecules

A: Probable 2-phosphosulfolactate phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,4236
Polymers56,0342
Non-polymers3894
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_566x,-y+1,-z+11
2
B: Probable 2-phosphosulfolactate phosphatase
C: Probable 2-phosphosulfolactate phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,3995
Polymers56,0342
Non-polymers3653
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2710 Å2
ΔGint-12 kcal/mol
Surface area18610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.686, 69.193, 453.518
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-444-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg label comp-ID: MSE / End label comp-ID: LEU / Refine code: 2 / Auth seq-ID: 1 - 235 / Label seq-ID: 13 - 247

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
DetailsBIOMOLECULE: 1,2 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 3 CHAIN(S). SEE FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). SIZE EXCLUSION CHROMATOGRAPHY (SEC) AND STATIC LIGHT SCATTERING SUPPORT THE ASSIGNMENT OF THE BIOLOGICAL OLIGOMERIZATION STATE AS A DIMER. GENERATING THE BIOMOLECULE COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. BIOMOLECULE: 1 APPLY THE FOLLOWING TO CHAINS: A BIOMT1 1 1.000000 0.000000 0.000000 0.00000 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 BIOMT1 2 1.000000 0.000000 0.000000 0.00000 BIOMT2 2 0.000000 -1.000000 0.000000 69.1930 BIOMT3 2 0.000000 0.000000 -1.000000 453.518 BIOMOLECULE: 2 APPLY THE FOLLOWING TO CHAINS: B, C BIOMT1 1 1.000000 0.000000 0.000000 0.00000 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 BIOMT3 1 0.000000 0.000000 1.000000 0.00000

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Components

#1: Protein Probable 2-phosphosulfolactate phosphatase


Mass: 28017.225 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium acetobutylicum (bacteria) / Gene: comB / Production host: Escherichia coli (E. coli)
References: UniProt: Q97E82, 2-phosphosulfolactate phosphatase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-3SL / (2R)-3-SULFOLACTIC ACID / (R)-2-HYDROXY-3-SULFOPROPANOIC ACID


Mass: 170.141 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H6O6S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 93 / 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: 2.33 Å3/Da / Density % sol: 46.9 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 7.5
Details: 20.0% PEG-8000, 0.1M HEPES pH 7.5, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.020035,0.979834
DetectorType: ADSC / Detector: CCD / Date: Sep 19, 2004
RadiationMonochromator: Double Crystal Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.0200351
20.9798341
ReflectionResolution: 2.49→50 Å / Num. obs: 22838 / % possible obs: 85.39 % / Redundancy: 4.5 % / Biso Wilson estimate: 50.62 Å2 / Rsym value: 0.048 / Net I/σ(I): 24.38
Reflection shellResolution: 2.49→2.53 Å / Redundancy: 1.34 % / Mean I/σ(I) obs: 3.19 / Num. unique all: 377 / Rsym value: 0.153 / % possible all: 29.22

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SHELXDphasing
autoSHARPphasing
REFMAC5.2.0005refinement
RefinementMethod to determine structure: MAD / Resolution: 2.49→38.7 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.924 / SU B: 19.135 / SU ML: 0.206 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.312
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) THE NOMINAL RESOLUTION OF THE DATA IS 2.6 A, WITH 1,104 OBSERVED REFLECTIONS ...Details: (1) HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. (2) ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. (3) THE NOMINAL RESOLUTION OF THE DATA IS 2.6 A, WITH 1,104 OBSERVED REFLECTIONS BETWEEN 2.6-2.49 A (34% COMPLETE FOR THIS SHELL) INCLUDED IN THE REFINEMENT.
RfactorNum. reflection% reflectionSelection details
Rfree0.22938 1159 5.1 %RANDOM
Rwork0.18994 ---
obs0.19201 21601 85.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.679 Å2
Baniso -1Baniso -2Baniso -3
1-3.6 Å20 Å20 Å2
2---0.27 Å20 Å2
3----3.33 Å2
Refinement stepCycle: LAST / Resolution: 2.49→38.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5478 0 32 93 5603
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0225565
X-RAY DIFFRACTIONr_bond_other_d0.0020.025219
X-RAY DIFFRACTIONr_angle_refined_deg1.5091.9877499
X-RAY DIFFRACTIONr_angle_other_deg0.829312187
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7725705
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.53925.656221
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.541151082
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5751521
X-RAY DIFFRACTIONr_chiral_restr0.0820.2900
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.026059
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021002
X-RAY DIFFRACTIONr_nbd_refined0.2110.21220
X-RAY DIFFRACTIONr_nbd_other0.1720.25259
X-RAY DIFFRACTIONr_nbtor_other0.0870.23533
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1480.2173
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1340.211
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2310.245
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.260.216
X-RAY DIFFRACTIONr_mcbond_it0.8211.53755
X-RAY DIFFRACTIONr_mcbond_other0.1661.51464
X-RAY DIFFRACTIONr_mcangle_it0.87425670
X-RAY DIFFRACTIONr_scbond_it1.74132259
X-RAY DIFFRACTIONr_scangle_it2.7334.51829
X-RAY DIFFRACTIONr_nbtor_refined0.180.22811
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1389tight positional0.040.05
2B1389tight positional0.040.05
3C1389tight positional0.040.05
1A2108medium positional0.220.5
2B2108medium positional0.270.5
3C2108medium positional0.280.5
1A1389tight thermal0.090.5
2B1389tight thermal0.080.5
3C1389tight thermal0.080.5
1A2108medium thermal0.52
2B2108medium thermal0.392
3C2108medium thermal0.412
LS refinement shellResolution: 2.488→2.552 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.317 36 6.32 %
Rwork0.251 534 -
obs--30.32 %
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)
12.0373-0.5148-1.0581.32540.59783.6230.04020.25070.0463-0.2352-0.058-0.07490.0934-0.11510.0178-0.25210.0184-0.0135-0.2262-0.0131-0.148823.571931.1688209.5029
20.81650.0469-0.3433.88262.1565.5828-0.0498-0.0753-0.02710.14580.0080.0981-0.0174-0.44560.0418-0.090.06790.0285-0.12090.0047-0.100911.690846.6136169.6232
31.44540.1007-0.68013.23590.09025.61380.11220.27850.0912-1.2646-0.09030.1109-0.1039-0.2555-0.02190.52870.03320.0133-0.0406-0.0289-0.093515.937242.7776134.8468
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 235
2X-RAY DIFFRACTION2B1 - 235
3X-RAY DIFFRACTION3C1 - 235

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