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- PDB-3fkh: Crystal structure of Putative pyridoxamine 5'-phosphate oxidase (... -

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Basic information

Entry
Database: PDB / ID: 3fkh
TitleCrystal structure of Putative pyridoxamine 5'-phosphate oxidase (NP_601736.1) from CORYNEBACTERIUM GLUTAMICUM ATCC 13032 KITASATO at 2.51 A resolution
ComponentsPutative pyridoxamine 5'-phosphate oxidase
KeywordsOXIDOREDUCTASE / NP_601736.1 / Putative pyridoxamine 5'-phosphate oxidase / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2 / unknown function
Function / homologyElectron Transport, Fmn-binding Protein; Chain A / Pnp Oxidase; Chain A / Roll / Mainly Beta / :
Function and homology information
Biological speciesCorynebacterium glutamicum ATCC 13032 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.51 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of Putative pyridoxamine 5'-phosphate oxidase (NP_601736.1) from CORYNEBACTERIUM GLUTAMICUM ATCC 13032 KITASATO at 2.51 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionDec 16, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 13, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Feb 1, 2023Group: Database references / Derived calculations / Structure summary
Category: chem_comp / database_2 ...chem_comp / database_2 / struct_ref_seq_dif / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 27, 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: _pdbx_entry_details.has_protein_modification / _struct_ncs_dom_lim.beg_auth_comp_id ..._pdbx_entry_details.has_protein_modification / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative pyridoxamine 5'-phosphate oxidase
B: Putative pyridoxamine 5'-phosphate oxidase
C: Putative pyridoxamine 5'-phosphate oxidase
D: Putative pyridoxamine 5'-phosphate oxidase
E: Putative pyridoxamine 5'-phosphate oxidase
F: Putative pyridoxamine 5'-phosphate oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,86815
Polymers95,9206
Non-polymers1,9489
Water1,40578
1
A: Putative pyridoxamine 5'-phosphate oxidase
B: Putative pyridoxamine 5'-phosphate oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,3003
Polymers31,9732
Non-polymers3261
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2890 Å2
ΔGint-15 kcal/mol
Surface area14410 Å2
MethodPISA
2
C: Putative pyridoxamine 5'-phosphate oxidase
D: Putative pyridoxamine 5'-phosphate oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,8507
Polymers31,9732
Non-polymers8775
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3840 Å2
ΔGint-14 kcal/mol
Surface area14400 Å2
MethodPISA
3
E: Putative pyridoxamine 5'-phosphate oxidase
F: Putative pyridoxamine 5'-phosphate oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,7185
Polymers31,9732
Non-polymers7453
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2880 Å2
ΔGint-17 kcal/mol
Surface area14050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.630, 88.310, 138.170
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
12B
22C
32D
42F

NCS domain segments:

Refine code: 5

Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111VALVALALAALAAA5 - 526 - 53
211VALVALALAALABB5 - 526 - 53
311VALVALALAALACC5 - 526 - 53
411VALVALALAALADD5 - 526 - 53
511VALVALALAALAEE5 - 526 - 53
611VALVALALAALAFF5 - 526 - 53
121HISHISLEULEUAA64 - 13065 - 131
221HISHISLEULEUBB64 - 13065 - 131
321HISHISLEULEUCC64 - 13065 - 131
421HISHISLEULEUDD64 - 13065 - 131
521HISHISLEULEUEE64 - 13065 - 131
621HISHISLEULEUFF64 - 13065 - 131
112GLUGLUSERSERBB53 - 5954 - 60
212GLUGLUSERSERCC53 - 5954 - 60
312GLUGLUSERSERDD53 - 5954 - 60
412GLUGLUSERSERFF53 - 5954 - 60

NCS ensembles :
ID
1
2
DetailsCRYSTAL PACKING ANALYSIS SUGGESTS THE ASSIGNMENT OF A DIMER AS THE SIGNIFICANT OLIGOMERIZATION STATE.

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Components

#1: Protein
Putative pyridoxamine 5'-phosphate oxidase


Mass: 15986.668 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium glutamicum ATCC 13032 (bacteria)
Gene: cg2794, NP_601736.1 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q6M2U2
#2: Chemical
ChemComp-P33 / 3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL / HEPTAETHYLENE GLYCOL / PEG330


Mass: 326.383 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C14H30O8 / Comment: precipitant*YM
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 78 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...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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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.37 Å3/Da / Density % sol: 48.17 %
Description: THE STATISTICS REPORTED IN REMARK 200 WERE COMPUTED WITH XSCALE WITH FRIEDEL PAIRS KEPT SEPARATE.
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.2000M Ca(OAc)2, 20.0000% PEG-8000, 0.1M MES pH 6.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.94645,0.97962
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 13, 2008 / Details: Adjustable focusing mirrors in K-B geometry
RadiationMonochromator: Si(111) Double Crystal Monochrometer / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.946451
20.979621
ReflectionResolution: 2.51→29.54 Å / Num. obs: 31540 / % possible obs: 96 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 52.655 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 15.98
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
2.5-2.590.296271714321169.8
2.59-2.690.2944.1194575882198.7
2.69-2.810.2175.5202235987199.2
2.81-2.960.1647.3215486220198.9
2.96-3.150.11110.6220756248199.1
3.15-3.390.08314.7218456017199.3
3.39-3.730.06320.7224836068199.1
3.73-4.260.05125.9225856035199.2
4.26-5.350.04331.3234036122199.2
5.35-29.540.04133.2238206155197.8

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3.006data extraction
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.51→29.54 Å / Cor.coef. Fo:Fc: 0.916 / Cor.coef. Fo:Fc free: 0.883 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 11.797 / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.681 / ESU R Free: 0.335
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. PEG-8000 FRAGMENTS (P33) FROM THE CRYSTALLIZATION SOLUTION ARE MODELED.
RfactorNum. reflection% reflectionSelection details
Rfree0.287 1601 5.1 %RANDOM
Rwork0.243 ---
obs0.245 31509 98.24 %-
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 max: 88.48 Å2 / Biso mean: 52.455 Å2 / Biso min: 14.92 Å2
Baniso -1Baniso -2Baniso -3
1-1.72 Å20 Å20 Å2
2---1.65 Å20 Å2
3----0.07 Å2
Refinement stepCycle: LAST / Resolution: 2.51→29.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6028 0 70 78 6176
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0226200
X-RAY DIFFRACTIONr_bond_other_d0.0030.024118
X-RAY DIFFRACTIONr_angle_refined_deg1.6471.9678411
X-RAY DIFFRACTIONr_angle_other_deg1.272310032
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.7425769
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.04324.196286
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.856151023
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.8271549
X-RAY DIFFRACTIONr_chiral_restr0.090.2991
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.026844
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021238
X-RAY DIFFRACTIONr_nbd_refined0.1480.2961
X-RAY DIFFRACTIONr_nbd_other0.1390.23988
X-RAY DIFFRACTIONr_nbtor_refined0.1490.22886
X-RAY DIFFRACTIONr_nbtor_other0.0680.23459
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1070.2170
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1180.219
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1610.276
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1330.25
X-RAY DIFFRACTIONr_mcbond_it1.29234017
X-RAY DIFFRACTIONr_mcbond_other0.45931554
X-RAY DIFFRACTIONr_mcangle_it2.24956232
X-RAY DIFFRACTIONr_scbond_it4.08782531
X-RAY DIFFRACTIONr_scangle_it5.743112177
LS refinement shellResolution: 2.507→2.572 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.368 98 -
Rwork0.325 1981 -
all-2079 -
obs--88.69 %

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