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- PDB-3on5: Crystal structure of a xanthine dehydrogenase (BH1974) from Bacil... -

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Basic information

Entry
Database: PDB / ID: 3on5
TitleCrystal structure of a xanthine dehydrogenase (BH1974) from Bacillus halodurans at 2.80 A resolution
ComponentsBH1974 protein
KeywordsOXIDOREDUCTASE / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-BIOLOGY
Function / homology
Function and homology information


: / BH1974-like, central domain / XdhC- CoxI / XdhC Rossmann domain / : / XdhC and CoxI family / XdhC Rossmann domain / NAD(P)-binding Rossmann-like Domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesBacillus halodurans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD, MOLECULAR REPLACEMENT / MAD, molecular replacement / Resolution: 2.8 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a xanthine dehydrogenase (BH1974) from Bacillus halodurans at 2.80 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionAug 27, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 15, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 20, 2011Group: Structure summary
Revision 1.3Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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 1.4Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.5Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BH1974 protein
B: BH1974 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,6444
Polymers83,5732
Non-polymers712
Water91951
1
A: BH1974 protein
B: BH1974 protein
hetero molecules

A: BH1974 protein
B: BH1974 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)167,2888
Polymers167,1464
Non-polymers1424
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_554y,x,-z-11
Buried area10440 Å2
ΔGint-84 kcal/mol
Surface area57090 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3900 Å2
ΔGint-36 kcal/mol
Surface area29860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.244, 94.244, 245.536
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein BH1974 protein


Mass: 41786.445 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus halodurans (bacteria) / Gene: 10174592, BH1974 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q9KBF4
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 51 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG.

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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: 3.26 Å3/Da / Density % sol: 62.29 %
Description: INITIAL PHASING WAS PERFORMED USING A ROSETTA-BASED APPROACH. PHASER WAS USED TO FIND AN ENSEMBLE OF CANDIDATE MOLECULAR REPLACEMENT SOLUTIONS USING COMPARATIVE MODELS BUILT BY ROSETTA ...Description: INITIAL PHASING WAS PERFORMED USING A ROSETTA-BASED APPROACH. PHASER WAS USED TO FIND AN ENSEMBLE OF CANDIDATE MOLECULAR REPLACEMENT SOLUTIONS USING COMPARATIVE MODELS BUILT BY ROSETTA BASED ON PDB ID 2WE8. ROSETTA WAS THEN USED TO REFINE THE CANDIDATE SOLUTION INTO DENSITY. THE SE SITES FROM THE MOLECULAR REPLACEMENT SOLUTION WERE USED AS AN INITIAL HEAVY ATOM MODEL FOR TWO-WAVELENGTH MAD PHASE REFINEMENT USING SHARP.
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 5.0% PEG-6000, 1.1M LiCl, 0.1M Citrate pH 5.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.978954,0.918370
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 4, 2006 / Details: Flat mirror (vertical focusing)
RadiationMonochromator: Single crystal Si(111) bent monochromator (horizontal focusing)
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9789541
20.918371
ReflectionResolution: 2.8→94.244 Å / Num. all: 28218 / Num. obs: 28218 / % possible obs: 99.9 % / Redundancy: 6.5 % / Biso Wilson estimate: 72.405 Å2 / Rsym value: 0.13 / Net I/σ(I): 12.6
Reflection shell

Rmerge(I) obs: 0.011 / Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.8-2.956.40.72572740441.10699.9
2.95-3.136.51.12461738050.6999.9
3.13-3.356.51.82326235930.42299.9
3.35-3.616.63.22216733650.23199.9
3.61-3.966.65.42058331060.13699.9
3.96-4.436.781908628440.09199.9
4.43-5.116.79.41692525290.074100
5.11-6.266.410.51392521620.06899.8
6.26-8.856.514.21115517220.04799.9
8.85-94.2446.120.9640610480.02799.6

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Phasing

PhasingMethod: MAD, molecular replacement

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Processing

Software
NameVersionClassificationNB
BUSTER-TNTBUSTER 2.8.0refinement
SCALA3.3.15data processing
PDB_EXTRACT3.1data extraction
MOSFLMdata reduction
SCALAdata scaling
Rosettaphasing
PHASERphasing
autoSHARPphasing
BUSTER2.8.0refinement
RefinementMethod to determine structure: MAD, MOLECULAR REPLACEMENT
Starting model: 2WE8

2we8


Resolution: 2.8→94.244 Å / Cor.coef. Fo:Fc: 0.9361 / Cor.coef. Fo:Fc free: 0.9256 / Occupancy max: 1 / Occupancy min: 0.5 / Cross valid method: THROUGHOUT / σ(F): 0
Details: 1. 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 ...Details: 1. 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. 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 3. ELECTRON DENSITIES CORRESPONDING TO RESIDUES 43-50 AND RESIDUES 84-94 ON THE B SUBUNIT WERE DISORDERED AND THESE REGIONS COULD NOT BE RELIABLY MODELED. 4. UN-EXPLAINED ELECTRON DENSITY NEAR THE SIDECHAIN OF CYS A92 WAS NOT MODELED. 5. THE REFINEMENT WAS RESTRAINED AGAINST THE TWO WAVELENGTH MAD PHASES. 6. NCS RESTRAINTS WERE APPLIED USING BUSTER'S LSSR RESTRAINT REPRESENTATION (-AUTONCS).
RfactorNum. reflection% reflectionSelection details
Rfree0.2218 1418 5.04 %RANDOM
Rwork0.1947 ---
obs0.1961 28132 --
Displacement parametersBiso max: 171.31 Å2 / Biso mean: 72.5282 Å2 / Biso min: 20.91 Å2
Baniso -1Baniso -2Baniso -3
1--1.7027 Å20 Å20 Å2
2---1.7027 Å20 Å2
3---3.4053 Å2
Refinement stepCycle: LAST / Resolution: 2.8→94.244 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5132 0 2 51 5185
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2390SINUSOIDAL8
X-RAY DIFFRACTIONt_trig_c_planes115HARMONIC2
X-RAY DIFFRACTIONt_gen_planes787HARMONIC5
X-RAY DIFFRACTIONt_it5302HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC8
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion701SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact5930SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d5302HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg7231HARMONIC21.12
X-RAY DIFFRACTIONt_omega_torsion3.41
X-RAY DIFFRACTIONt_other_torsion2.1
LS refinement shellResolution: 2.8→2.91 Å / Total num. of bins used: 14
RfactorNum. reflection% reflection
Rfree0.2562 136 4.72 %
Rwork0.2393 2745 -
all0.2401 2881 -
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)
10.52260.5170.55512.68350.86292.16190.1530.2958-0.0849-0.0334-0.0323-0.37460.18810.3923-0.1207-0.20440.0166-0.02110.023-0.0359-0.1081-7.7431-29.8872-146.777
20.76331.21670.40912.71211.21.02720.2014-0.1704-0.22580.3997-0.1216-0.06580.5230.0641-0.07980.11890.0033-0.208-0.16320.045-0.0886-13.7974-54.1025-124.607
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A1 - 336
2X-RAY DIFFRACTION2{ B|* }B-2 - 338

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