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- PDB-2hti: CRYSTAL STRUCTURE OF A FLAVIN-NUCLEOTIDE-BINDING PROTEIN (BH_0577... -

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Basic information

Entry
Database: PDB / ID: 2hti
TitleCRYSTAL STRUCTURE OF A FLAVIN-NUCLEOTIDE-BINDING PROTEIN (BH_0577) FROM BACILLUS HALODURANS AT 2.50 A RESOLUTION
ComponentsBH0577 protein
KeywordsFMN-BINDING PROTEIN / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-2
Function / homology
Function and homology information


Pyridoxamine 5'-phosphate oxidase-related / Pyridoxamine 5'-phosphate oxidase / Electron Transport, Fmn-binding Protein; Chain A / Pnp Oxidase; Chain A / FMN-binding split barrel / Roll / Mainly Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / BH0577 protein
Similarity search - Component
Biological speciesBacillus halodurans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of BH0577 (10173191) from Bacillus halodurans at 2.50 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJul 25, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 1, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / 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
Remark 300BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S) ...BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 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 OLIGIMERIZATION 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

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Assembly

Deposited unit
A: BH0577 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,9583
Polymers21,1491
Non-polymers8092
Water36020
1
A: BH0577 protein
hetero molecules

A: BH0577 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,9166
Polymers42,2992
Non-polymers1,6174
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+5/61
Buried area4890 Å2
ΔGint-56 kcal/mol
Surface area11410 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)72.170, 72.170, 129.981
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
DetailsSIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF A DIMER AS A BIOLOGICALLY SIGNIFICANT OLIGIMERIZATION STATE.

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Components

#1: Protein BH0577 protein


Mass: 21149.336 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus halodurans (bacteria) / Gene: 10173191 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9KFA8
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 20 / 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: 3.43 Å3/Da / Density % sol: 63.88 %
Crystal growTemperature: 293 K
Details: 22.0% PEG-3350, 0.15M NaThioCyanate, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.92522,0.97934
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jun 5, 2006 / Details: Flat collimating mirror, toroid focusing mirror
RadiationMonochromator: Double crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.925221
20.979341
ReflectionResolution: 2.3→28.831 Å / Num. obs: 7389 / % possible obs: 99.7 % / Redundancy: 13.6 % / Rmerge(I) obs: 0.098 / Rsym value: 0.098 / Net I/σ(I): 5.2
Reflection shell

Rmerge(I) obs: 0.015 / Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.42-2.4814.40.584475860.0150799.7
2.48-2.5514.20.579185580.0130799.5
2.55-2.6214.10.777945540.0104499.8
2.62-2.7114.31.175325280.65999.6
2.71-2.7914.11.573455220.599.9
2.79-2.8914.11.872095120.41399.5
2.89-313.92.567994890.29399.9
3-3.12143.266754780.22699.7
3.12-3.2613.94.261884460.16999.7
3.26-3.4213.85.761184420.1299.7
3.42-3.6113.56.558364310.10199.7
3.61-3.8313.57.652943910.08499.8
3.83-4.0913.48.449433700.07499.8
4.09-4.4213.39.147043550.06899.9
4.42-4.8412.9943483360.06599.9
4.84-5.4112.910.138312980.06199.9
5.41-6.2512.49.334592780.06599.9
6.25-7.65127.928512380.07599.8
7.65-10.8211.310.221521910.05899.8
10.82-28.839.612.511101160.04894.1

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
SHELXphasing
REFMAC5.2.0005refinement
SCALAdata scaling
PDB_EXTRACT2data extraction
MOSFLMdata reduction
CCP4(SCALA)data scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.5→28.831 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.915 / SU B: 7.855 / SU ML: 0.175 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.309 / ESU R Free: 0.254
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 INCORP- ORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORP- ORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.7 TO ACCOUNT FOR THE REDUCED SCATTERING DUE TO PARTIAL S-MET INCORPORATION. 3. A FLAVIN ADENINE DINUCLEOTIDE (FAD) MOLECULE WAS LOCATED IN THE STRUCTURE. 4. RESIDUES 0-9, 80-92, 126-142, AND 166-184 WERE NOT MODELED DUE POOR ELECTRON DENSITY. 5. EXTRA DENSITY WAS NOTED NEAR RESIDUE I109 BUT NOT MODELED. 6. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.262 346 4.7 %RANDOM
Rwork0.208 ---
obs0.21 7389 99.42 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 57.979 Å2
Baniso -1Baniso -2Baniso -3
1-1.55 Å20.78 Å20 Å2
2--1.55 Å20 Å2
3----2.33 Å2
Refinement stepCycle: LAST / Resolution: 2.5→28.831 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms943 0 54 20 1017
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0221019
X-RAY DIFFRACTIONr_bond_other_d0.0010.02902
X-RAY DIFFRACTIONr_angle_refined_deg1.5472.0161390
X-RAY DIFFRACTIONr_angle_other_deg0.67532077
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.535123
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.43323.61136
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.9115152
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.38154
X-RAY DIFFRACTIONr_chiral_restr0.0760.2159
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021082
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02194
X-RAY DIFFRACTIONr_nbd_refined0.2250.3170
X-RAY DIFFRACTIONr_nbd_other0.2170.3822
X-RAY DIFFRACTIONr_nbtor_refined0.2050.5490
X-RAY DIFFRACTIONr_nbtor_other0.0930.5579
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2070.570
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1550.36
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1830.330
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1520.510
X-RAY DIFFRACTIONr_mcbond_it1.7413624
X-RAY DIFFRACTIONr_mcbond_other0.2373255
X-RAY DIFFRACTIONr_mcangle_it3.34551001
X-RAY DIFFRACTIONr_scbond_it4.7138439
X-RAY DIFFRACTIONr_scangle_it7.11111389
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.437 17 -
Rwork0.266 505 -
obs-522 99.43 %
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)
15.34290.3298-1.45098.4959-0.65554.5739-0.0401-0.1517-0.19320.73030.2013-0.05430.00780.0955-0.16110.43530.0151-0.05090.32740.02580.231530.28616.77460.44
23.83383.5438-1.59168.8156-1.47972.59980.0023-0.1030.21150.92480.36980.7111-0.2866-0.1413-0.37210.52010.08530.01310.41620.0490.304727.53717.94764.658
33.03913.2531-0.16616.77931.51097.76680.0732-0.21230.12340.56640.23980.2351-0.4660.2625-0.3130.39190.06340.03480.35760.03230.321429.67117.4562.262
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA10 - 7911 - 80
2X-RAY DIFFRACTION2AA93 - 12594 - 126
3X-RAY DIFFRACTION3AA143 - 165144 - 166

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