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- PDB-2i51: CRYSTAL STRUCTURE OF a pyridoxamine 5'-phosphate oxidase-related,... -

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Entry
Database: PDB / ID: 2i51
TitleCRYSTAL STRUCTURE OF a pyridoxamine 5'-phosphate oxidase-related, FMN binding protein (NPUN_F5749) FROM NOSTOC PUNCTIFORME PCC 73102 AT 1.40 A RESOLUTION
ComponentsUncharacterized conserved protein of COG5135
KeywordsFLAVOPROTEIN / PYRIDOXAMINE 5'-PHOSPHATE OXIDASE-RELATED PROTEIN / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-2
Function / homology
Function and homology information


pyridoxamine phosphate oxidase activity / pyridoxine biosynthetic process / FMN binding
Similarity search - Function
Pyridoxamine 5'-phosphate oxidase, probable FMN-dependent, Alr4036 family / Pyridoxamine 5'-phosphate oxidase, Alr4036 family, FMN-binding domain / Pyridoxamine 5'-phosphate oxidase / 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 / Alr4036 protein
Similarity search - Component
Biological speciesNostoc punctiforme (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.4 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of Uncharacterized conserved protein of COG5135 (ZP_00109616.1) from Nostoc punctiforme PCC 73102 at 1.40 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionAug 23, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 5, 2006Provider: 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 1.4Oct 25, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Remark 300BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S) ...BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). SIZE EXCLUSION CHROMATOGRAPHY DATA SUPPORTS THE ASSIGNMENT OF A DIMER AS A BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION 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. A suitable database reference was not available at the time of processing.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uncharacterized conserved protein of COG5135
B: Uncharacterized conserved protein of COG5135
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,63825
Polymers45,3922
Non-polymers2,24623
Water6,467359
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9850 Å2
ΔGint36 kcal/mol
Surface area16600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.647, 65.928, 112.380
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
DetailsSIZE EXCLUSION CHROMATOGRAPHY DATA SUPPORTS THE ASSIGNMENT OF A DIMER AS A BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE.

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Components

#1: Protein Uncharacterized conserved protein of COG5135


Mass: 22695.977 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nostoc punctiforme (bacteria) / Strain: PCC 73102 / Gene: ZP_00109616.1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8YQ04, UniProt: B2J933*PLUS
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 359 / 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: 2.7 Å3/Da / Density % sol: 54.04 %
Crystal growTemperature: 277 K
Details: 20.0% Glycerol, 24.0% PEG-1500, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K

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Data collection

Diffraction
IDCrystal-ID
21
11
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSSRL BL1-510.978489
SYNCHROTRONSSRL BL11-120.979264,0.911617
Detector
TypeIDDetectorDateDetails
ADSC QUANTUM 3151CCDJul 7, 20061m long Rh coated bent cylindrical mirror forhorizontal and vertical focussing
ADSC QUANTUM 3152CCDJul 2, 2006Flat 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
10.9784891
20.9792641
30.9116171
ReflectionResolution: 1.397→29.386 Å / Num. obs: 96246 / % possible obs: 99.7 % / Redundancy: 5.2 % / Biso Wilson estimate: 15.91 Å2 / Rmerge(I) obs: 0.113 / Rsym value: 0.113 / Net I/σ(I): 3.5
Reflection shell

Rmerge(I) obs: 0.01 / Diffraction-ID: 2

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.4-1.444.60.73189669100.0101698
1.44-1.484.70.83217868990.874100
1.48-1.524.713139867160.758100
1.52-1.574.71.23056165130.604100
1.57-1.624.71.52943862770.488100
1.62-1.674.71.52883661190.395100
1.67-1.744.72.32794859390.31799.9
1.74-1.814.72.92660156530.254100
1.81-1.894.73.92589355080.184100
1.89-1.984.74.72447251990.14299.8
1.98-2.094.76.22325549440.10799.8
2.09-2.216.43.63047547490.157100
2.21-2.376.44.42871144800.135100
2.37-2.566.44.52646741350.126100
2.56-2.86.35.12406438230.116100
2.8-3.136.15.42132235030.10999.9
3.13-3.615.86.21756230520.09298.7
3.61-4.436.47.81683826360.0799.6
4.43-6.266.18.21241520490.06799.2
6.26-29.445.79.3652011420.06694.1

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
SHELXphasing
REFMAC5.2.0019refinement
SCALAdata scaling
PDB_EXTRACT2data extraction
MOSFLMdata reduction
CCP4(SCALA)data scaling
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.4→29.386 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.963 / SU B: 1.907 / SU ML: 0.038 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.052 / ESU R Free: 0.054
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 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 4. RESIDUES B134-137 ARE DISORDERED AND WERE NOT MODELED. 5. FMN MODELED BASED ON PROPOSED FUNCTION AND DENSITY. 6. ETHYLENE GLYCOL AND GLYCEROL MODELED BASED ON CRYSTALLIAZTION CONDITIONS. 7. THERE IS UNMODELED DENSITY NEAR A45, A115, AND B153.
RfactorNum. reflection% reflectionSelection details
Rfree0.188 4853 5 %RANDOM
Rwork0.165 ---
obs0.166 96170 99.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.71 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2--0.45 Å20 Å2
3----0.44 Å2
Refinement stepCycle: LAST / Resolution: 1.4→29.386 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3120 0 148 359 3627
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0223453
X-RAY DIFFRACTIONr_bond_other_d0.0020.022455
X-RAY DIFFRACTIONr_angle_refined_deg1.6371.9794706
X-RAY DIFFRACTIONr_angle_other_deg0.97435908
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5415414
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.68622.989174
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.1615519
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9051536
X-RAY DIFFRACTIONr_chiral_restr0.1070.2480
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.023799
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02717
X-RAY DIFFRACTIONr_nbd_refined0.2130.2631
X-RAY DIFFRACTIONr_nbd_other0.2270.22783
X-RAY DIFFRACTIONr_nbtor_refined0.1890.21636
X-RAY DIFFRACTIONr_nbtor_other0.0860.21895
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1660.2288
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.310.217
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3310.246
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1930.29
X-RAY DIFFRACTIONr_mcbond_it2.13532069
X-RAY DIFFRACTIONr_mcbond_other0.5063768
X-RAY DIFFRACTIONr_mcangle_it3.06553251
X-RAY DIFFRACTIONr_scbond_it4.32181684
X-RAY DIFFRACTIONr_scangle_it6.091111440
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.347 318 -
Rwork0.323 6569 -
obs-6887 97.94 %
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)
10.22450.20980.08720.52160.30821.0564-0.04550.05650.0301-0.0911-0.01290.0541-0.08170.00310.0585-0.03760.0012-0.0072-0.0460.0014-0.038948.027962.10664.2312
20.48490.09010.12570.68780.44651.139-0.0204-0.07640.0620.0024-0.05460.1077-0.1309-0.0390.075-0.0276-0.00090.0093-0.0591-0.0142-0.023447.254373.097924.3294
Refinement TLS group

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

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA1 - 1942 - 195
22BB0 - 1941 - 195

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