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- PDB-2o8q: CRYSTAL STRUCTURE OF A PROTEIN WITH A CUPIN-LIKE FOLD AND UNKNOWN... -

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Basic information

Entry
Database: PDB / ID: 2o8q
TitleCRYSTAL STRUCTURE OF A PROTEIN WITH A CUPIN-LIKE FOLD AND UNKNOWN FUNCTION (BXE_C0505) FROM BURKHOLDERIA XENOVORANS LB400 AT 1.55 A RESOLUTION
ComponentsHypothetical protein
KeywordsMETAL BINDING PROTEIN / CPUIN-LIKE FOLD / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-2
Function / homology
Function and homology information


Cupin 2, conserved barrel / Cupin domain / RmlC-like cupin domain superfamily / Jelly Rolls / RmlC-like jelly roll fold / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
NICKEL (II) ION / Cupin type-2 domain-containing protein
Similarity search - Component
Biological speciesBurkholderia xenovorans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.55 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of hypothetical protein (YP_555756.1) from Burkholderia xenovorans LB400 at 1.55 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionDec 12, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 26, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations ...Advisory / Derived calculations / 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 / 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.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
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 TETRAMER AS A BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE.
Remark 999SEQUENCE 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)30,79512
Polymers30,1812
Non-polymers61410
Water4,161231
1
A: Hypothetical protein
B: Hypothetical protein
hetero molecules

A: Hypothetical protein
B: Hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,59024
Polymers60,3624
Non-polymers1,22820
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area13120 Å2
ΔGint-83 kcal/mol
Surface area21260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.255, 102.255, 74.746
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212
DetailsSIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF A TETRAMER AS A BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE.

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Components

#1: Protein Hypothetical protein


Mass: 15090.426 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia xenovorans (bacteria) / Strain: LB400 / Gene: YP_555756.1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q13HN3
#2: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 231 / 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

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)Description
13.2461.98TWO CRYSTALS WERE USED FOR THE SOLUTION OF THIS STRUCTURE. A 2.35 ANGSTROM MAD DATA COLLECTED FROM ONE CRYSTAL WAS USED TO PHASE AND TRACE AN INITIAL MODEL. TH E MODEL WAS THEN REFINED USING THE AMPLITUDES FROM A SECOND CRYSTAL THAT DIFFRAC TED TO AN ENHANCED RESOLUTION OF 1.55 ANGSTROM. THE 2.35 ANGSTROM MAD PHASES FRO M THE FIRST CRYSTAL WERE USED AS PHASE RESTRAINTS DURING THE REFINEMENT.
2TWO CRYSTALS WERE USED FOR THE SOLUTION OF THIS STRUCTURE. A 2.35 ANGSTROM MAD DATA COLLECTED FROM ONE CRYSTAL WAS USED TO PHASE AND TRACE AN INITIAL MODEL. TH E MODEL WAS THEN REFINED USING THE AMPLITUDES FROM A SECOND CRYSTAL THAT DIFFRAC TED TO AN ENHANCED RESOLUTION OF 1.55 ANGSTROM. THE 2.35 ANGSTROM MAD PHASES FRO M THE FIRST CRYSTAL WERE USED AS PHASE RESTRAINTS DURING THE REFINEMENT.
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2771vapor diffusion, sitting drop, nanodrop92.0% Dioxane, 10.0% PEG-20000, 0.1M Bicine pH 9.0, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K
2772vapor diffusion, sitting drop, nanodrop6.60.2M (NH4)2Tartrate, 20.0% PEG-3350, No Buffer pH 6.6, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21002
Diffraction source
SourceSiteBeamlineIDWavelengthWavelength (Å)
SYNCHROTRONSSRL BL1-511.000017
SYNCHROTRONAPS 23-ID-D20.97921, 0.97888, 0.94645
Detector
TypeIDDetectorDateDetails
ADSC QUANTUM 3151CCDNov 17, 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
20.979211
30.978881
40.946451
ReflectionResolution: 1.55→29.683 Å / Num. obs: 57924 / % possible obs: 100 % / Redundancy: 9.1 % / Biso Wilson estimate: 21.35 Å2 / Rmerge(I) obs: 0.067 / Rsym value: 0.067 / Net I/σ(I): 7.5
Reflection shell

Diffraction-ID: 1,2

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.55-1.5970.9650.82908941570.96599.7
1.59-1.6370.7412873941080.74100
1.63-1.6870.5831.32803740160.583100
1.68-1.7370.4491.72739839160.449100
1.73-1.7970.3332.32634337670.333100
1.79-1.8570.2373.22547336470.237100
1.85-1.926.90.1814.12469835540.181100
1.92-270.1494.82367634040.149100
2-2.096.90.1325.22267832820.132100
2.09-2.1970.1046.42174731210.104100
2.19-2.31110.1454.63291429960.145100
2.31-2.4512.90.1325.13673428410.132100
2.45-2.6213.90.1076.43717826800.107100
2.62-2.8313.70.08383424524970.083100
2.83-3.113.50.06510.23136823250.065100
3.1-3.4712.80.05212.12690221010.052100
3.47-413.80.0415.62581418740.04100
4-4.913.20.03914.42116916090.039100
4.9-6.9312.50.04413.11591412750.044100
6.93-29.6810.90.0321882267540.03298.6

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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
MOSFLMdata reduction
CCP4(SCALA)data scaling
SHELXDphasing
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.55→29.683 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.957 / SU B: 1.898 / SU ML: 0.038 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.059 / ESU R Free: 0.061
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: (1). HYDROGENS HAVE BEEN ADDED IN RIDING POSITIONS. (2). ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. (3). A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING ...Details: (1). HYDROGENS HAVE BEEN ADDED IN 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 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. (4). A NI ATOM ON EACH OF THE TWO SUBUNITS IN THE ASYMMETRIC UNIT IS COORDINATED TO THE SIDE CHAIN OF HIS 58, HIS 60, HIS 100, AND THREE WATERS. ANOMALOUS DIFFERENCE FOURIERS AND X-RAY FLUORESCENCE EXPERIMENTS SUPPORT THE ASSIGNMENT THE NI IONS. (5). RESIDUES 20-21 AND 50-54 ON THE A SUBUNIT AND 20-22 ON THE B SUBUNIT ARE DISORDERED AND WERE NOT MODELED.
RfactorNum. reflection% reflectionSelection details
Rfree0.191 2939 5.1 %RANDOM
Rwork0.17 ---
obs0.171 57868 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.305 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å20 Å2
2---0.03 Å20 Å2
3---0.05 Å2
Refinement stepCycle: LAST / Resolution: 1.55→29.683 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1900 0 34 231 2165
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0212081
X-RAY DIFFRACTIONr_bond_other_d0.0020.021399
X-RAY DIFFRACTIONr_angle_refined_deg1.8371.9332820
X-RAY DIFFRACTIONr_angle_other_deg1.00633378
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.1185262
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.54123.558104
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.65215308
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.631514
X-RAY DIFFRACTIONr_chiral_restr0.1140.2295
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022398
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02460
X-RAY DIFFRACTIONr_nbd_refined0.2020.2382
X-RAY DIFFRACTIONr_nbd_other0.2090.21486
X-RAY DIFFRACTIONr_nbtor_refined0.1830.2970
X-RAY DIFFRACTIONr_nbtor_other0.0870.21146
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1830.2173
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.280.220
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3730.262
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.240.215
X-RAY DIFFRACTIONr_mcbond_it2.06231305
X-RAY DIFFRACTIONr_mcbond_other0.5163525
X-RAY DIFFRACTIONr_mcangle_it3.18352049
X-RAY DIFFRACTIONr_scbond_it4.5048878
X-RAY DIFFRACTIONr_scangle_it6.46411771
LS refinement shellResolution: 1.55→1.59 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 238 -
Rwork0.255 3968 -
obs-4206 99.83 %
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)
11.86290.2744-0.95991.2727-0.27041.3598-0.00710.1220.0451-0.15510.0188-0.1713-0.05480.0596-0.0117-0.04170.00070.0366-0.03780.0026-0.043134.63819.842823.6197
21.20460.3174-0.36192.012-0.22641.257-0.0521-0.1354-0.13650.0670.0268-0.12650.18770.11670.0253-0.04960.0409-0.0009-0.03960.0255-0.039532.01357.488440.5619
Refinement TLS group

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

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA0 - 1281 - 129
22BB1 - 1272 - 128

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