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- PDB-2p11: CRYSTAL STRUCTURE OF A PUTATIVE HALOACID DEHALOGENASE-LIKE HYDROL... -

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Basic information

Entry
Database: PDB / ID: 2p11
TitleCRYSTAL STRUCTURE OF A PUTATIVE HALOACID DEHALOGENASE-LIKE HYDROLASE (BXE_B1342) FROM BURKHOLDERIA XENOVORANS LB400 AT 2.20 A RESOLUTION
ComponentsHypothetical protein
KeywordsHYDROLASE / PUTATIVE HALOACID DEHALOGENASE-LIKE HYDROLASE / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-2
Function / homology
Function and homology information


GTP Cyclohydrolase I; Chain A, domain 1 - #50 / GTP Cyclohydrolase I; Chain A, domain 1 / HAD superfamily/HAD-like / haloacid dehalogenase-like hydrolase / HAD superfamily / HAD-like superfamily / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Haloacid dehalogenase-like hydrolase
Similarity search - Component
Biological speciesBurkholderia xenovorans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of hypothetical protein (YP_553970.1) from Burkholderia xenovorans LB400 at 2.20 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionMar 1, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 20, 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 1.4Oct 25, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.5Jan 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
Revision 1.6Nov 13, 2024Group: Data collection / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id
Remark 300 BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 ... BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). SIZE EXCLUSION CHROMATOGRAPHY AND STATIC LIGHT SCATTERING SUPPORT THE ASSIGNMENT OF A DIMER AS A BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE.
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 (0) 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: Hypothetical protein
B: Hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,5289
Polymers53,9972
Non-polymers5317
Water1,874104
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4070 Å2
ΔGint-33 kcal/mol
Surface area18200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.390, 68.080, 88.240
Angle α, β, γ (deg.)90.000, 112.220, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: PRO / Beg label comp-ID: PRO / End auth comp-ID: MSE / End label comp-ID: MSE / Refine code: 4 / Auth seq-ID: 8 - 220 / Label seq-ID: 9 - 221

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
DetailsSIZE EXCLUSION CHROMATOGRAPHY AND STATIC SUPPORT THE ASSIGNMENT OF A DIMER AS A BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE.

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Components

#1: Protein Hypothetical protein


Mass: 26998.547 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia xenovorans (bacteria) / Strain: LB400 / Gene: YP_553970.1, Bxeno_B1652, Bxe_B1342 / Plasmid: speedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q13MR9
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 104 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.07 Å3/Da / Density % sol: 40.55 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: NANODROP, 25.0% Glycerol, 0.6M KH2PO4, 0.6M NaH2PO4, 0.1M HEPES pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.94642, 0.97925, 0.97902
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Feb 8, 2007 / Details: Flat mirror (vertical focusing)
RadiationMonochromator: Single crystal Si(111) bent (horizontal focusing)
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.946421
20.979251
30.979021
ReflectionResolution: 2.2→28.341 Å / Num. obs: 22404 / % possible obs: 94.2 % / Biso Wilson estimate: 47.699 Å2 / Rmerge(I) obs: 0.035 / Net I/σ(I): 13.88
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique all% possible all
2.2-2.270.292.85582346476.4
2.27-2.360.2393.37255407993.3
2.36-2.470.2063.97675432394.6
2.47-2.60.1515.27496420094.5
2.6-2.760.1216.57441416795.1
2.76-2.970.0868.97645427797
2.97-3.270.051147888441398.1
3.27-3.740.0321.97864438198.9
3.740.01931.47961438599

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
SHELXphasing
REFMAC5.2.0019refinement
XSCALEdata scaling
PDB_EXTRACT2data extraction
MAR345CCDdata collection
XDSdata reduction
SHELXDphasing
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.2→28.341 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.928 / SU B: 19.299 / SU ML: 0.226 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.324 / ESU R Free: 0.228
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. GOL AND CL ARE MODELED BASED ON CRYSTALLIZATION AND CRYO CONDITIONS. 5. THE FOLLOWING REGIONS HAVE VERY POOR DENSITIES: A51-A62, A190-A206, B39-B63 AND B192-B204. 6. THERE ARE SOME RESIDUAL DENSITIES IN THE PUTATIVE ACTIVE SITES NEAR RESIDUES 16, 18. THEY ARE NOT MODELED DUE TO THE POOR DENSITY.
RfactorNum. reflection% reflectionSelection details
Rfree0.247 1148 5.1 %RANDOM
Rwork0.201 ---
all0.203 ---
obs0.203 22404 99.2 %-
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: 13.155 Å2
Baniso -1Baniso -2Baniso -3
1-5.92 Å20 Å23 Å2
2---2.2 Å20 Å2
3----1.45 Å2
Refinement stepCycle: LAST / Resolution: 2.2→28.341 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3448 0 32 104 3584
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0223561
X-RAY DIFFRACTIONr_bond_other_d0.0030.022436
X-RAY DIFFRACTIONr_angle_refined_deg1.4121.9644827
X-RAY DIFFRACTIONr_angle_other_deg0.94835869
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1985433
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.44322.663169
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.53215573
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2721533
X-RAY DIFFRACTIONr_chiral_restr0.080.2527
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023952
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02770
X-RAY DIFFRACTIONr_nbd_refined0.2150.2798
X-RAY DIFFRACTIONr_nbd_other0.1940.22496
X-RAY DIFFRACTIONr_nbtor_refined0.1850.21685
X-RAY DIFFRACTIONr_nbtor_other0.0880.21886
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1880.2110
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2250.226
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2070.261
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0460.22
X-RAY DIFFRACTIONr_mcbond_it1.70432223
X-RAY DIFFRACTIONr_mcbond_other0.5023874
X-RAY DIFFRACTIONr_mcangle_it2.49153474
X-RAY DIFFRACTIONr_scbond_it4.51381523
X-RAY DIFFRACTIONr_scangle_it5.971111352
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 2802 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
MEDIUM POSITIONAL0.480.5
MEDIUM THERMAL0.852
LS refinement shellResolution: 2.2→2.254 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.31 77 -
Rwork0.265 1438 -
obs-1515 93.23 %
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)
12.3072-0.0654-0.74014.605-2.814.117-0.09540.0321-0.31130.68230.08160.30340.2082-0.1060.01380.22750.01110.0911-0.2202-0.0047-0.213340.175617.269738.1412
25.223-0.3631-5.75795.71821.82386.70340.0958-0.0469-0.32840.30710.0757-0.09410.00760.0375-0.1716-0.3558-0.074-0.1682-0.0523-0.0156-0.209242.29423.244112.6636
33.24831.1452-1.48754.5414-0.79233.9114-0.08660.2119-0.0304-0.0417-0.1097-0.4863-0.1730.06890.1963-0.4771-0.0432-0.1229-0.17560.0136-0.190360.78540.3592.1525
40.78661.2784-0.07269.6423-4.84763.40040.0152-0.263-0.4240.5802-0.2688-1.13450.2590.52030.25370.005-0.0468-0.18270.00940.03020.020260.917232.109525.9371
Refinement TLS group

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

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA8 - 239 - 24
21AA91 - 22792 - 228
32AA24 - 9025 - 91
43BB8 - 239 - 24
53BB91 - 22292 - 223
64BB24 - 9025 - 91

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