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- PDB-3db0: Crystal structure of Putative Pyridoxamine 5'-phosphate oxidase (... -

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Basic information

Entry
Database: PDB / ID: 3db0
TitleCrystal structure of Putative Pyridoxamine 5'-phosphate oxidase (NP_472219.1) from LISTERIA INNOCUA at 2.00 A resolution
ComponentsLin2891 protein
KeywordsOXIDOREDUCTASE / NP_472219.1 / Putative Pyridoxamine 5'-phosphate oxidase / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
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 / Lin2891 protein
Function and homology information
Biological speciesListeria innocua (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of Putative Pyridoxamine 5'-phosphate oxidase (NP_472219.1) from LISTERIA INNOCUA at 2.00 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionMay 30, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 29, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_struct_assembly_auth_evidence / 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 / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Oct 16, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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: Lin2891 protein
B: Lin2891 protein


Theoretical massNumber of molelcules
Total (without water)29,2082
Polymers29,2082
Non-polymers00
Water1,964109
1
A: Lin2891 protein
B: Lin2891 protein

A: Lin2891 protein
B: Lin2891 protein


Theoretical massNumber of molelcules
Total (without water)58,4164
Polymers58,4164
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area5500 Å2
ΔGint-43 kcal/mol
Surface area24610 Å2
MethodPISA
2
A: Lin2891 protein
B: Lin2891 protein

A: Lin2891 protein
B: Lin2891 protein


Theoretical massNumber of molelcules
Total (without water)58,4164
Polymers58,4164
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area5680 Å2
ΔGint-39 kcal/mol
Surface area24430 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, light scattering, homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1770 Å2
ΔGint-17 kcal/mol
Surface area13280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.160, 42.230, 62.020
Angle α, β, γ (deg.)90.000, 91.590, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31A
41B
51A
61B

NCS domain segments:

Ens-ID: 1 / Refine code: 4

Dom-IDComponent-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA4 - 474 - 47
21BB4 - 474 - 47
32AA64 - 9464 - 94
42BB64 - 9464 - 94
53AA111 - 126111 - 126
63BB111 - 126111 - 126
DetailsAUTHORS STATE THAT SIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF AN DIMER AS A SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION. THE DIMER IS CONSISTENT AN ANALYSIS OF CRYSTAL PACKING AND A SIMILAR DIMER IS PREDICTED TO BE A STABLE FOR SEVERAL HOMOLOGS.

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Components

#1: Protein Lin2891 protein


Mass: 14604.106 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria innocua (bacteria) / Gene: lin2891 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q926Z8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 109 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE CONSTRUCT INCLUDES AMINO ACIDS 1-127 OF THE FULL LENGTH PROTEIN CONSISTING OF 139 RESIDUES AND ...THE CONSTRUCT INCLUDES AMINO ACIDS 1-127 OF THE FULL LENGTH PROTEIN CONSISTING OF 139 RESIDUES AND 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: 2.07 Å3/Da / Density % sol: 40.44 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.57
Details: 40.9% 1,2-propanediol, 0.1M sodium acetate pH 4.57, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.91837,0.97956,0.97908
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Apr 13, 2008 / 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
10.918371
20.979561
30.979081
ReflectionResolution: 2→26.055 Å / Num. obs: 16307 / % possible obs: 98.1 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 26.246 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 8.88
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
2-2.070.4591.854902885192.9
2.07-2.150.3792.358693059198.7
2.15-2.250.2732.962073211198.9
2.25-2.370.2313.561443185199.2
2.37-2.520.1764.561563185199
2.52-2.710.1455.759833086199
2.71-2.990.0878.762643228198.9
2.99-3.420.05213.660593109198.5
3.42-4.30.03320.460603098198.3
4.3-26.060.02525.161273130197.9

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.4.0067refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3.004data extraction
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2→26.055 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.93 / SU B: 8.466 / SU ML: 0.119 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.191 / ESU R Free: 0.175
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2.ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3.A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN ...Details: 1.HYDROGENS HAVE BEEN ADDED IN THE 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.
RfactorNum. reflection% reflectionSelection details
Rfree0.239 828 5.1 %RANDOM
Rwork0.182 ---
obs0.185 16307 99.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.25 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å20 Å2-1.27 Å2
2--0.32 Å20 Å2
3----0.43 Å2
Refinement stepCycle: LAST / Resolution: 2→26.055 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1863 0 0 109 1972
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0221929
X-RAY DIFFRACTIONr_bond_other_d0.0010.021256
X-RAY DIFFRACTIONr_angle_refined_deg1.7251.9622630
X-RAY DIFFRACTIONr_angle_other_deg1.00533094
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.9785242
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.05125.11984
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.32615316
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.793157
X-RAY DIFFRACTIONr_chiral_restr0.0990.2305
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212144
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02363
X-RAY DIFFRACTIONr_mcbond_it1.94231213
X-RAY DIFFRACTIONr_mcbond_other0.7253485
X-RAY DIFFRACTIONr_mcangle_it3.19351967
X-RAY DIFFRACTIONr_scbond_it5.5788716
X-RAY DIFFRACTIONr_scangle_it8.19411663
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 1104 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
MEDIUM POSITIONAL0.510.5
MEDIUM THERMAL1.692
LS refinement shellResolution: 1.999→2.051 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.248 61 -
Rwork0.205 1100 -
all-1161 -
obs--97.81 %
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)
11.5534-0.61750.18291.6881-0.00420.9667-0.00790.0117-0.1494-0.00570.0678-0.03930.14950.1567-0.0599-0.00250.0402-0.01810.0422-0.03590.003516.972810.190813.2338
20.8808-0.53790.26320.77750.58271.63680.0223-0.0049-0.01750.0139-0.01850.02650.023-0.0816-0.0037-0.061-0.00020.003-0.09370.0103-0.0652-2.919222.954318.0694
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 1262 - 127
2X-RAY DIFFRACTION2BB4 - 1275 - 128

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