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- PDB-2o08: CRYSTAL STRUCTURE OF A PUTATIVE HD SUPERFAMILY HYDROLASE (BH1327)... -

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Basic information

Entry
Database: PDB / ID: 2o08
TitleCRYSTAL STRUCTURE OF A PUTATIVE HD SUPERFAMILY HYDROLASE (BH1327) FROM BACILLUS HALODURANS AT 1.90 A RESOLUTION
ComponentsBH1327 protein
KeywordsHYDROLASE / PUTATIVE HD SUPERFAMILY HYDROLASE / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-2
Function / homology
Function and homology information


bis(5'-nucleosyl)-tetraphosphatase (symmetrical) / hydrolase activity / nucleotide binding / metal ion binding
Similarity search - Function
Ap4A hydrolase / : / Hypothetical protein af1432 / Hypothetical protein af1432 / HD domain profile. / HD domain / HD domain / Metal dependent phosphohydrolases with conserved 'HD' motif. / HD/PDEase domain / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
2'-DEOXYGUANOSINE-5'-DIPHOSPHATE / : / NITRATE ION / PHOSPHATE ION / Unknown ligand / Bis(5'-nucleosyl)-tetraphosphatase, symmetrical
Similarity search - Component
Biological speciesBacillus halodurans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of hypothetical protein (NP_242193.1) from Bacillus halodurans at 1.90 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionNov 27, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 19, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / 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 / 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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_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.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
Revision 1.6Oct 9, 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 300BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S) ...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 WITH STATIC LIGHT SCATTERING SUPPORTS 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: BH1327 protein
B: BH1327 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,75617
Polymers43,5892
Non-polymers2,16715
Water5,855325
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5370 Å2
ΔGint-75 kcal/mol
Surface area17640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.830, 166.510, 73.410
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-581-

HOH

21A-658-

HOH

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

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MSE / Beg label comp-ID: MSE / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: 6 / Auth seq-ID: 1 - 184 / Label seq-ID: 2 - 185

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

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein BH1327 protein


Mass: 21794.340 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus halodurans (bacteria) / Gene: NP_242193.1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9KD90

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Non-polymers , 7 types, 340 molecules

#2: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 1 / Source method: obtained synthetically
#5: Chemical
ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#6: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO3
#7: Chemical ChemComp-DGI / 2'-DEOXYGUANOSINE-5'-DIPHOSPHATE


Type: DNA linking / Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 325 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.04 Å3/Da / Density % sol: 59.58 %
Description: THE PHASE RESTRAINTS FROM A DIFFERENT CRYSTAL WERE USED IN THE REFINEMENT OF THIS DATASET.
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop, nanodrop
Details: 0.2M potassium nitrate, 20.0% polyethylene glycol 3350, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelengthWavelength (Å)
SYNCHROTRONSSRL BL1-511.000017
SYNCHROTRONAPS 23-ID-D20.97942, 0.97921, 0.94645
Detector
TypeIDDetectorDateDetails
ADSC QUANTUM 3151CCDNov 10, 20061m long Rh coated bent cylindrical mirror forhorizontal and vertical focussing
MARMOSAIC 300 mm CCD2CCDOct 20, 2006Adjustable focusing mirrors in K-B geometry
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si(111) Double Crystal MonochromatorSINGLE WAVELENGTHMx-ray1
2Si(111) Double Crystal MonochromatorMADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
11.0000171
20.979421
30.979211
40.946451
ReflectionResolution: 1.9→28.88 Å / Num. obs: 41676 / % possible obs: 93.6 % / Biso Wilson estimate: 31.858 Å2 / Rmerge(I) obs: 0.086 / Net I/σ(I): 10.48
Reflection shell

Diffraction-ID: 1,2

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique all% possible all
1.9-1.970.5182.113215655578.9
1.97-2.050.412.815129712986.7
2.05-2.140.3113.815122704690.3
2.14-2.250.2934.919017736793.2
2.25-2.390.2426.121499770095.1
2.39-2.580.1858.325727807096.7
2.58-2.840.13310.926960795097.7
2.84-3.250.08814.626610793698.6
3.250.05921.526096798099.4

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
SHARPphasing
REFMAC5.2.0019refinement
XSCALEdata scaling
PDB_EXTRACT2data extraction
XDSdata reduction
SHELXphasing
RefinementMethod to determine structure: MAD / Resolution: 1.9→28.88 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.94 / SU B: 6.477 / SU ML: 0.099 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.126 / ESU R Free: 0.129
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. 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. 3. MODELING OF FE IONS IS SUPPORTED BY METAL EXCITATION SCAN. 4. NO3 AND PEG 200 (PG4) MOLECULES FROM THE CRYSTALLIZATION AND CRYO SOLUTIONS (RESPECTIVELY) ARE MODELED. 5. A 2'-DEOXYGUANOSINE 5'-DIPHOSPHATE (DGI) MOLECULE WAS MODELED IN CHAIN B NEAR THE DI-IRON SITE. THE ASSIGNMENT WAS BASED ON THE DENSITY, PFAM ANNOTATION AND SIMILAR STRUCTURES. THE DENSITY IN CHAIN A NEAR THE DI-IRON SITE WAS NOT AS CLEAR AND WAS MODELED AS A PHOSPHATE AND UNKNOWN LIAGND (UNL). 6. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.223 2112 5.1 %RANDOM
Rwork0.174 ---
obs0.176 41665 98.62 %-
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: 30.733 Å2
Baniso -1Baniso -2Baniso -3
1-1.05 Å20 Å20 Å2
2---2.83 Å20 Å2
3---1.77 Å2
Refinement stepCycle: LAST / Resolution: 1.9→28.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2997 0 119 325 3441
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0223245
X-RAY DIFFRACTIONr_bond_other_d0.0030.022240
X-RAY DIFFRACTIONr_angle_refined_deg1.6051.9964381
X-RAY DIFFRACTIONr_angle_other_deg1.1835478
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.3115395
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.38624.14157
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.29615568
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3711523
X-RAY DIFFRACTIONr_chiral_restr0.0940.2486
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023527
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02652
X-RAY DIFFRACTIONr_nbd_refined0.2190.2791
X-RAY DIFFRACTIONr_nbd_other0.170.22407
X-RAY DIFFRACTIONr_nbtor_refined0.180.21577
X-RAY DIFFRACTIONr_nbtor_other0.0840.21595
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1390.2272
X-RAY DIFFRACTIONr_metal_ion_refined0.0960.22
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1220.210
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1690.233
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2020.213
X-RAY DIFFRACTIONr_mcbond_it2.22732132
X-RAY DIFFRACTIONr_mcbond_other0.5573764
X-RAY DIFFRACTIONr_mcangle_it3.03853077
X-RAY DIFFRACTIONr_scbond_it5.40181460
X-RAY DIFFRACTIONr_scangle_it7.188111292
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 2451 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
LOOSE POSITIONAL0.475
LOOSE THERMAL2.7110
LS refinement shellResolution: 1.901→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.344 178 -
Rwork0.282 2702 -
obs-2880 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)
10.4435-0.2976-0.2481.20310.15850.13870.03310.0132-0.00510.018-0.01750.0546-0.0146-0.0258-0.0156-0.06280.0114-0.0031-0.085-0.0089-0.152961.76418.965.638
20.4552-0.6090.09280.822-0.1630.2270.03980.02990.0785-0.0774-0.0678-0.11310.0319-0.01620.028-0.09140.01790.0353-0.08730.0182-0.110149.31454.8123.943
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL / Auth seq-ID: 0 - 186 / Label seq-ID: 1 - 187

IDRefine TLS-IDAuth asym-IDLabel asym-ID
11AA
22BB

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