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- PDB-3ro7: Crystal Structure of Mouse Apolipoprotein A-I Binding Protein in ... -

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Basic information

Entry
Database: PDB / ID: 3ro7
TitleCrystal Structure of Mouse Apolipoprotein A-I Binding Protein in Complex with Thymine.
ComponentsApolipoprotein A-I-binding protein
KeywordsPROTEIN BINDING / ROSSMANN FOLD
Function / homology
Function and homology information


membrane raft distribution / NAD(P)H-hydrate epimerase / NADHX epimerase activity / NADPHX epimerase activity / regulation of cholesterol efflux / nicotinamide nucleotide metabolic process / Nicotinamide salvaging / sprouting angiogenesis / lipid transport / negative regulation of angiogenesis ...membrane raft distribution / NAD(P)H-hydrate epimerase / NADHX epimerase activity / NADPHX epimerase activity / regulation of cholesterol efflux / nicotinamide nucleotide metabolic process / Nicotinamide salvaging / sprouting angiogenesis / lipid transport / negative regulation of angiogenesis / cilium / cell body / nucleotide binding / mitochondrion / extracellular space / extracellular region / identical protein binding / metal ion binding
Similarity search - Function
YjeF N-terminal domain-containing protein NAXE-like / YjeF N-terminal domain / YjeF N-terminal domain superfamily / YjeF-related protein N-terminus / YjeF N-terminal domain / YjeF N-terminal domain profile. / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
THYMINE / NAD(P)H-hydrate epimerase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsShumilin, I.A. / Jha, K.N. / Cymborowski, M. / Herr, J.C. / Minor, W.
CitationJournal: Structure / Year: 2012
Title: Identification of unknown protein function using metabolite cocktail screening.
Authors: Shumilin, I.A. / Cymborowski, M. / Chertihin, O. / Jha, K.N. / Herr, J.C. / Lesley, S.A. / Joachimiak, A. / Minor, W.
History
DepositionApr 25, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 18, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 31, 2012Group: Database references
Revision 1.2Apr 13, 2022Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _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 1.3Sep 13, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Apolipoprotein A-I-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,0953
Polymers29,8731
Non-polymers2222
Water48627
1
A: Apolipoprotein A-I-binding protein
hetero molecules

A: Apolipoprotein A-I-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,1906
Polymers59,7462
Non-polymers4444
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation17_555x-y+1/3,-y+2/3,-z+2/31
Buried area2770 Å2
ΔGint-17 kcal/mol
Surface area18900 Å2
MethodPISA
2
A: Apolipoprotein A-I-binding protein
hetero molecules

A: Apolipoprotein A-I-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,1906
Polymers59,7462
Non-polymers4444
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556y,x,-z+11
Buried area1600 Å2
ΔGint-9 kcal/mol
Surface area20070 Å2
MethodPISA
3
A: Apolipoprotein A-I-binding protein
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)180,57118
Polymers179,2386
Non-polymers1,33312
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation4_556y,x,-z+11
crystal symmetry operation5_556x-y,-y,-z+11
crystal symmetry operation6_556-x,-x+y,-z+11
Buried area9380 Å2
ΔGint-47 kcal/mol
Surface area55640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.291, 126.291, 109.472
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32

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Components

#1: Protein Apolipoprotein A-I-binding protein / AI-BP


Mass: 29872.963 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Aibp, Apoa1bp / Plasmid: PET21A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8K4Z3
#2: Chemical ChemComp-TDR / THYMINE / Thymine


Mass: 126.113 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H6N2O2
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 27 / 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: 2.81 Å3/Da / Density % sol: 56.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.1 M SODIUM ACETATE, 1.5 M AMMONIUM SULFATE, PH 4.6, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 273K, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97935 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 2, 2007 / Details: MIRROR
RadiationMonochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97935 Å / Relative weight: 1
ReflectionAv R equivalents: 0.162 / Number: 125076
ReflectionResolution: 2.5→50 Å / Num. all: 125076 / Num. obs: 125076 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 10.7 % / Biso Wilson estimate: 44.2 Å2 / Rmerge(I) obs: 0.162 / Rsym value: 0.162 / Net I/σ(I): 21.875
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 9.7 % / Rmerge(I) obs: 0.746 / Mean I/σ(I) obs: 2.694 / Rsym value: 0.746 / % possible all: 99.6
Cell measurementReflection used: 125076

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0109refinement
PDB_EXTRACT3.006data extraction
HKL-3000data collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2o8n

2o8n


Resolution: 2.5→50 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.93 / Occupancy max: 1 / Occupancy min: 1 / SU B: 16.393 / SU ML: 0.173 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.237 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS; U VALUES: RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.228 557 4.8 %RANDOM
Rwork0.175 ---
obs0.178 11704 99.72 %-
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: 96.97 Å2 / Biso mean: 45.999 Å2 / Biso min: 22.88 Å2
Baniso -1Baniso -2Baniso -3
1--3.35 Å2-1.68 Å20 Å2
2---3.35 Å20 Å2
3---5.03 Å2
Refinement stepCycle: LAST / Resolution: 2.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1808 0 14 27 1849
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0221872
X-RAY DIFFRACTIONr_bond_other_d00.021275
X-RAY DIFFRACTIONr_angle_refined_deg1.6592.0022550
X-RAY DIFFRACTIONr_angle_other_deg4.08933135
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.685232
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.07324.66775
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.84815301
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.667156
X-RAY DIFFRACTIONr_chiral_restr0.1010.2278
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212057
X-RAY DIFFRACTIONr_gen_planes_other0.0070.02352
X-RAY DIFFRACTIONr_mcbond_it0.7381.51169
X-RAY DIFFRACTIONr_mcbond_other01.5460
X-RAY DIFFRACTIONr_mcangle_it1.40721900
X-RAY DIFFRACTIONr_scbond_it2.7343703
X-RAY DIFFRACTIONr_scangle_it4.0374.5650
LS refinement shellResolution: 2.504→2.569 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.287 41 -
Rwork0.249 794 -
all-835 -
obs--97.09 %
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)
17.09348.87393.019918.33335.54445.148-0.25140.3901-0.6037-1.39580.5747-1.30570.11030.1717-0.32330.51140.00090.11720.1678-0.01840.097812.44726.68519.671
21.17871.0858-1.02783.5758-2.07262.15010.0961-0.01380.08290.05090.0230.2599-0.1089-0.0845-0.11910.2106-0.0153-0.00470.13190.0180.03492.71128.17238.442
31.70871.3210.27033.1554-0.60111.74420.02730.002-0.2099-0.1231-0.0615-0.25120.00780.06660.03420.1393-0.00980.01010.07870.01540.06211.00319.17643.541
40.56960.04540.10442.403-1.55662.10080.00470.1142-0.0776-0.79450.12390.16690.4151-0.1551-0.12860.358-0.0625-0.04040.1117-0.0130.04152.36320.48927.779
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A26 - 46
2X-RAY DIFFRACTION2A47 - 77
3X-RAY DIFFRACTION3A78 - 170
4X-RAY DIFFRACTION4A171 - 258

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