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- PDB-2hq7: Crystal structure of Protein related to general stress protein 26... -

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Basic information

Entry
Database: PDB / ID: 2hq7
TitleCrystal structure of Protein related to general stress protein 26(GS26) of B.subtilis (pyridoxinephosphate oxidase family) (NP_350077.1) from CLOSTRIDIUM ACETOBUTYLICUM at 2.00 A resolution
ComponentsProtein, related to general stress protein 26(GS26) of B.subtilis
KeywordsOXIDOREDUCTASE / NP_350077.1 / Protein related to general stress protein 26(GS26) of B.subtilis (pyridoxinephosphate oxidase family) / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI
Function / homology: / Pyridoxamine 5'-phosphate oxidase, putative / Pyridoxamine 5'-phosphate oxidase / Electron Transport, Fmn-binding Protein; Chain A / Pnp Oxidase; Chain A / FMN-binding split barrel / Roll / Mainly Beta / Protein, related to general stress protein 26(GS26) of B.subtilis (Pyridoxinephosphate oxidase family)
Function and homology information
Biological speciesClostridium acetobutylicum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of Protein related to general stress protein 26(GS26) of B.subtilis (pyridoxinephosphate oxidase family) (NP_350077.1) from CLOSTRIDIUM ACETOBUTYLICUM at 2.00 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJul 18, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 15, 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 1.4Jan 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 1.5Oct 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 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: Protein, related to general stress protein 26(GS26) of B.subtilis
B: Protein, related to general stress protein 26(GS26) of B.subtilis
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,0738
Polymers34,7542
Non-polymers3196
Water2,540141
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3560 Å2
ΔGint-27 kcal/mol
Surface area13870 Å2
MethodPISA
2
A: Protein, related to general stress protein 26(GS26) of B.subtilis
B: Protein, related to general stress protein 26(GS26) of B.subtilis
hetero molecules

A: Protein, related to general stress protein 26(GS26) of B.subtilis
B: Protein, related to general stress protein 26(GS26) of B.subtilis
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,14616
Polymers69,5074
Non-polymers63812
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area8860 Å2
ΔGint-88 kcal/mol
Surface area26620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.850, 36.790, 97.970
Angle α, β, γ (deg.)90.000, 113.750, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Protein, related to general stress protein 26(GS26) of B.subtilis / Pyridoxinephosphate oxidase family


Mass: 17376.869 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium acetobutylicum (bacteria) / Gene: NP_350077.1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q97DI6
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


Mass: 18.015 Da / Num. of mol.: 141 / 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: 40.1 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 7
Details: 0.2M Ca(OAc)2, 20.0% PEG-3000, 0.1M TRIS pH 7.0, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97934, 0.91837
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jun 19, 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
10.979341
20.918371
ReflectionResolution: 2→29.235 Å / Num. obs: 19245 / % possible obs: 93.1 % / Biso Wilson estimate: 33.345 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 7.87
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique allDiffraction-ID% possible all
2-2.070.392257612980181.9
2.07-2.150.3262.462723218188.2
2.15-2.250.256366923417190.4
2.25-2.370.2283.367233442191.7
2.37-2.520.1734.268503501193
2.52-2.710.1435.167353457194.8
2.71-2.990.0927.372023698196.7
2.99-3.420.0551170453628198.3
3.42-29.2350.03516.271033660199.1

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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
XDSdata reduction
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2→29.235 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.923 / SU B: 10.679 / SU ML: 0.145 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.209 / ESU R Free: 0.18
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. RESIDUES A1, A143-145, B1, AND B144-145 ARE DISORDERED AND NOT INCLUDED IN THE MODEL. 4. EDO AND CL FROM THE CRYSTALLIZATION/CRYO SOLUTION ARE MODELED. 5. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.242 985 5.1 %RANDOM
Rwork0.191 ---
all0.193 ---
obs0.19347 19244 99.59 %-
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: 31.614 Å2
Baniso -1Baniso -2Baniso -3
1--1.97 Å20 Å2-0.5 Å2
2--3.14 Å20 Å2
3----1.57 Å2
Refinement stepCycle: LAST / Resolution: 2→29.235 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2274 0 18 141 2433
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0222349
X-RAY DIFFRACTIONr_bond_other_d0.0010.021589
X-RAY DIFFRACTIONr_angle_refined_deg1.411.9533167
X-RAY DIFFRACTIONr_angle_other_deg0.83233879
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3135283
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.02624.717106
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.85915423
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.288158
X-RAY DIFFRACTIONr_chiral_restr0.0820.2347
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022562
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02475
X-RAY DIFFRACTIONr_nbd_refined0.1880.2435
X-RAY DIFFRACTIONr_nbd_other0.1940.21575
X-RAY DIFFRACTIONr_nbtor_refined0.1880.21124
X-RAY DIFFRACTIONr_nbtor_other0.0910.21327
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.180.2136
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1750.217
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1740.232
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1670.215
X-RAY DIFFRACTIONr_mcbond_it2.61631449
X-RAY DIFFRACTIONr_mcbond_other0.6083577
X-RAY DIFFRACTIONr_mcangle_it3.57552268
X-RAY DIFFRACTIONr_scbond_it6.2481064
X-RAY DIFFRACTIONr_scangle_it7.71711898
LS refinement shellResolution: 2→2.051 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.281 66 -
Rwork0.264 1326 -
obs-1392 97.21 %
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)
10.9959-0.7125-0.42920.75370.03770.7719-0.0276-0.07670.0550.0229-0.0229-0.0565-0.03190.04690.0505-0.0072-0.0104-0.0049-0.04020.0341-0.0189-12.612.76432.277
21.627-0.1091-0.30880.41150.56811.4238-0.0251-0.05620.0705-0.1281-0.03590.0668-0.01280.04180.06090.01830.0066-0.018-0.12050.01620.0028-7.966-5.42912.888
Refinement TLS group

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

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA2 - 1423 - 143
22BB2 - 1433 - 144

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