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- PDB-2ou5: Crystal structure of a pyridoxamine 5'-phosphate oxidase-related ... -

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Basic information

Entry
Database: PDB / ID: 2ou5
TitleCrystal structure of a pyridoxamine 5'-phosphate oxidase-related fmn-binding protein (jann_0254) from jannaschia sp. ccs1 at 1.60 A resolution
ComponentsPyridoxamine 5'-phosphate oxidase-related, FMN-binding
KeywordsFLAVOPROTEIN / Split barrel-like fold / structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


Pyridoxamine 5'-phosphate oxidase, Alr4036 family, FMN-binding domain / 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 MONONUCLEOTIDE / Pyridoxamine 5'-phosphate oxidase-related FMN-binding protein
Similarity search - Component
Biological speciesJannaschia sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.6 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of pyridoxamine 5'-phosphate oxidase-related FMN-binding (YP_508196.1) from Jannaschia sp. CCS1 at 1.60 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionFeb 9, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 6, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Source and taxonomy / 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 1.5Nov 20, 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 999 SEQUENCE 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

Downloads & links

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Assembly

Deposited unit
A: Pyridoxamine 5'-phosphate oxidase-related, FMN-binding
B: Pyridoxamine 5'-phosphate oxidase-related, FMN-binding
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,0979
Polymers38,7202
Non-polymers1,3777
Water7,440413
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5770 Å2
ΔGint-42 kcal/mol
Surface area16480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.880, 68.510, 111.920
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Pyridoxamine 5'-phosphate oxidase-related, FMN-binding


Mass: 19359.811 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Jannaschia sp. (bacteria) / Strain: CCS1 / Gene: YP_508196.1, Jann_0254 / Plasmid: speedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q28VU1
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 413 / 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: 2.27 Å3/Da / Density % sol: 45.8 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 9
Details: NANODROP, 1.6M (NH4)2SO4, 0.1M Bicine pH 9.0, 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: 0.91162, 0.97922, 0.97898
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Feb 1, 2007 / Details: Flat mirror (vertical focusing)
RadiationMonochromator: Single crystal Si(111) bent (horizontal focusing)
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.911621
20.979221
30.978981
ReflectionResolution: 1.6→28.94 Å / Num. obs: 46954 / % possible obs: 95 % / Biso Wilson estimate: 24.807 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 12.43
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique all% possible all
1.6-1.660.2992.415169793184.4
1.66-1.720.2562.814300741090.8
1.72-1.80.2053.516482853892.6
1.8-1.90.1544.817171892094.1
1.9-2.020.1096.916602864396
2.02-2.170.0729.716237849398.1
2.17-2.390.0513.417102890098.4
2.39-2.730.041717008880798.7
2.730.02625.317274894799

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
SHELXphasing
REFMAC5.2.0005refinement
XSCALEdata scaling
PDB_EXTRACT2data extraction
MAR345CCDdata collection
XDSdata reduction
SHELXDphasing
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.6→28.94 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.944 / SU B: 4.179 / SU ML: 0.075 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.094 / ESU R Free: 0.098
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. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 4. FMN MODELED BASED ON PROPOSED FUNCTION AND HOMOLOGS. 5. SO4 AND GOL MODELED BASED ON CRYSTALLIZATION AND CRYO CONDITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.221 2370 5.1 %RANDOM
Rwork0.178 ---
all0.181 ---
obs0.181 46899 99.18 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.781 Å2
Baniso -1Baniso -2Baniso -3
1-0.1 Å20 Å20 Å2
2--1.5 Å20 Å2
3----1.6 Å2
Refinement stepCycle: LAST / Resolution: 1.6→28.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2693 0 91 413 3197
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0212948
X-RAY DIFFRACTIONr_bond_other_d0.0030.022713
X-RAY DIFFRACTIONr_angle_refined_deg1.6221.9824068
X-RAY DIFFRACTIONr_angle_other_deg0.87736283
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2195372
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.17322.017119
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.97215430
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2281527
X-RAY DIFFRACTIONr_chiral_restr0.0890.2459
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023229
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02575
X-RAY DIFFRACTIONr_nbd_refined0.2010.2523
X-RAY DIFFRACTIONr_nbd_other0.1960.22803
X-RAY DIFFRACTIONr_nbtor_refined0.1730.21397
X-RAY DIFFRACTIONr_nbtor_other0.0840.21720
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1510.2270
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2240.215
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2220.290
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2150.217
X-RAY DIFFRACTIONr_mcbond_it2.17431942
X-RAY DIFFRACTIONr_mcbond_other0.5973702
X-RAY DIFFRACTIONr_mcangle_it2.88652943
X-RAY DIFFRACTIONr_scbond_it4.3481331
X-RAY DIFFRACTIONr_scangle_it5.671111113
LS refinement shellResolution: 1.6→1.64 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.299 157 -
Rwork0.248 3143 -
obs-3300 95.35 %
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)
10.3839-0.0141-0.29650.51430.51141.95990.05010.03640.038-0.0418-0.0353-0.0236-0.2462-0.1325-0.0148-0.0150.0038-0.0132-0.06760.0103-0.024533.338245.07769.9463
20.5269-0.2405-0.20930.33290.39261.9250.00170.0442-0.02090.0411-0.0392-0.00060.0892-0.07820.0375-0.0532-0.0037-0.0061-0.05550.0029-0.018239.15425.569368.7289
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL / Auth seq-ID: 0 - 174 / Label seq-ID: 1 - 175

IDRefine TLS-IDAuth asym-IDLabel asym-ID
11AA
22BB

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