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- PDB-2iab: Crystal structure of a protein with FMN-binding split barrel fold... -

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Basic information

Entry
Database: PDB / ID: 2iab
TitleCrystal structure of a protein with FMN-binding split barrel fold (NP_828636.1) from Streptomyces avermitilis at 2.00 A resolution
ComponentsHypothetical protein
KeywordsUNKNOWN FUNCTION / NP_828636.1 / hypothetical protein / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI
Function / homologyPyridoxamine 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 / ISOPROPYL ALCOHOL / Pyridoxamine 5'-phosphate oxidase N-terminal domain-containing protein
Function and homology information
Biological speciesStreptomyces avermitilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of hypothetical protein (NP_828636.1) from STREPTOMYCES AVERMITILIS at 2.00 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionSep 7, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 19, 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 1.4Oct 9, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ncs_dom_lim / 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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
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 SUPPORTS THE ASSIGNMENT OF A DIMER AS A BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE.
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: Hypothetical protein
B: Hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,3246
Polymers34,0842
Non-polymers2404
Water4,216234
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2780 Å2
ΔGint-8 kcal/mol
Surface area15210 Å2
MethodPISA
2
A: Hypothetical protein
B: Hypothetical protein
hetero molecules

A: Hypothetical protein
B: Hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,64812
Polymers68,1674
Non-polymers4818
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_666-y+1,-x+1,-z+7/61
Buried area10490 Å2
ΔGint-19 kcal/mol
Surface area25480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.890, 87.890, 151.580
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31A
41B
51A
61B
71A
81B

NCS domain segments:

Ens-ID: 1 / Refine code: 4

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11THRTHRLEULEUAA2 - 743 - 75
21THRTHRLEULEUBB2 - 743 - 75
32GLUGLUGLUGLUAA86 - 9387 - 94
42GLUGLUGLUGLUBB86 - 9387 - 94
53PHEPHEGLUGLUAA105 - 135106 - 136
63PHEPHEGLUGLUBB105 - 135106 - 136
74MSEMSELEULEUAA145 - 151146 - 152
84MSEMSELEULEUBB145 - 151146 - 152

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Components

#1: Protein Hypothetical protein


Mass: 17041.775 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces avermitilis (bacteria) / Gene: NP_828636.1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q825J7
#2: Chemical
ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 234 / 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: 2.35 Å3/Da / Density % sol: 47.28 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 5.6
Details: 20.0% iso-Propanol, 20.0% PEG-4000, 0.1M Citrate pH 5.6, 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: 0.91162,0.97936,0.97920
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jun 18, 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
10.911621
20.979361
30.97921
ReflectionResolution: 2→34.001 Å / Num. obs: 24072 / % possible obs: 100 % / Redundancy: 14 % / Biso Wilson estimate: 31.69 Å2 / Rmerge(I) obs: 0.077 / Χ2: 0.942 / Net I/σ(I): 14.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2-2.0512.30.68816720.9411100
2.05-2.1113.70.55416761.0231100
2.11-2.1714.30.47516811.0561100
2.17-2.2414.40.36716981.0751100
2.24-2.3214.40.29816771.1461100
2.32-2.4114.50.25516941.0021100
2.41-2.5214.40.21416940.9671100
2.52-2.6514.40.16817081.0381100
2.65-2.8214.40.11917091.0191100
2.82-3.0414.30.08817260.9841100
3.04-3.3414.30.0717240.821100
3.34-3.8314.10.05317570.7251100
3.83-4.8213.90.04217820.771100
4.82-5012.80.0419320.636199.5

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
SOLVEphasing
REFMAC5.2.0005refinement
SCALEPACKdata scaling
PDB_EXTRACT2data extraction
DENZOdata reduction
RefinementMethod to determine structure: MAD / Resolution: 2→34.001 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.932 / SU B: 6.288 / SU ML: 0.094 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.163 / ESU R Free: 0.157
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.FOUR ISOPROPANOL MOLECULES FROM CRYSTALLIZATION ARE BUILT IN THE MODEL. 4.A MET- ...Details: 1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 2.ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY 3.FOUR ISOPROPANOL MOLECULES FROM CRYSTALLIZATION ARE BUILT IN THE MODEL. 4.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. 5.AN ANOMALOUS DIFFERENCE DENSITY PEAK IS LOCATED BETWEEN THE SIDECHAINS OF TRP A133 AND ASP B25. THE POSITION OF THIS ANOMALOUS DIFFERENCE PEAK CORRESPONDS TO THE LOCATION OF THE SE ATOM OF MSE B1 IF THE NCS TRANSFORMATION RELATING SUBUNIT B TO SUBUNIT A IS APPLIED. HOWEVER, DISORDER AT THE N-TERMINUS OF THE A SUBUNIT PREVENTED MODELING OF RESIDUES A0 and A1. 6.WATER MOLECULES WERE MODELED INTO UNEXPLAINED DENSITY NEAR THR A79.
RfactorNum. reflection% reflectionSelection details
Rfree0.23 1196 5 %RANDOM
Rwork0.178 ---
all0.18 ---
obs0.18 24057 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.924 Å2
Baniso -1Baniso -2Baniso -3
1-0.51 Å20.26 Å20 Å2
2--0.51 Å20 Å2
3----0.77 Å2
Refinement stepCycle: LAST / Resolution: 2→34.001 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2302 0 16 234 2552
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0222385
X-RAY DIFFRACTIONr_bond_other_d0.0020.022222
X-RAY DIFFRACTIONr_angle_refined_deg1.6361.9853258
X-RAY DIFFRACTIONr_angle_other_deg0.89135118
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9285306
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.58722.65398
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.72415356
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7651526
X-RAY DIFFRACTIONr_chiral_restr0.0920.2369
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022683
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02489
X-RAY DIFFRACTIONr_nbd_refined0.2130.2400
X-RAY DIFFRACTIONr_nbd_other0.20.22109
X-RAY DIFFRACTIONr_nbtor_refined0.1790.21089
X-RAY DIFFRACTIONr_nbtor_other0.0860.21458
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1420.2168
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2240.218
X-RAY DIFFRACTIONr_symmetry_vdw_other0.320.281
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1940.220
X-RAY DIFFRACTIONr_mcbond_it2.20431546
X-RAY DIFFRACTIONr_mcbond_other0.793621
X-RAY DIFFRACTIONr_mcangle_it3.1952446
X-RAY DIFFRACTIONr_scbond_it5.0758954
X-RAY DIFFRACTIONr_scangle_it6.76411811
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 1730 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
MEDIUM POSITIONAL0.530.5
MEDIUM THERMAL1.282
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.284 86 -
Rwork0.217 1623 -
obs-1709 99.48 %
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)
11.41820.0604-0.07711.02920.01881.61350.00970.02350.03610.0067-0.0070.0967-0.0141-0.0634-0.0027-0.1226-0.0146-0.0008-0.1009-0.0174-0.10423.6121.309476.7609
22.32580.0922-0.24961.67360.67642.1659-0.0031-0.05240.07320.41730.06110.0750.1595-0.2068-0.0580.03110.00350.0236-0.049-0.0078-0.052218.28222.709397.689
Refinement TLS group

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

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA2 - 1543 - 155
22BB1 - 1512 - 152

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