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- PDB-4ck4: Ovine beta-Lactoglobulin at Atomic Resolution -

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Basic information

Entry
Database: PDB / ID: 4ck4
TitleOvine beta-Lactoglobulin at Atomic Resolution
ComponentsBETA_LACTOGLOBULIN-1/B
KeywordsTRANSPORT PROTEIN / OVINE-LACTOGLOBULIN / HIGH RESOLUTION
Function / homology
Function and homology information


retinol binding / extracellular space
Similarity search - Function
Beta-lactoglobulin / Lipocalin / Lipocalin family conserved site / Calycin beta-barrel core domain / Lipocalin / cytosolic fatty-acid binding protein family / Lipocalin/cytosolic fatty-acid binding domain / Calycin / Lipocalin / Lipocalin signature. / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
ACETATE ION / AMMONIUM ION / Beta-lactoglobulin-1/B
Similarity search - Component
Biological speciesOVIS ARIES (sheep)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.12 Å
AuthorsKontopidis, G. / Nordle, A. / Sawyer, L.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2014
Title: Ovine Beta-Lactoglobulin at Atomic Resolution
Authors: Kontopidis, G. / Nordle Gilliver, A. / Sawyer, L.
History
DepositionDec 27, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 8, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 12, 2014Group: Database references
Revision 1.2Feb 25, 2015Group: Database references
Revision 1.3May 27, 2015Group: Atomic model / Other
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BETA_LACTOGLOBULIN-1/B
B: BETA_LACTOGLOBULIN-1/B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,26329
Polymers36,3942
Non-polymers86927
Water8,575476
1
A: BETA_LACTOGLOBULIN-1/B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,61414
Polymers18,1971
Non-polymers41713
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: BETA_LACTOGLOBULIN-1/B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,64915
Polymers18,1971
Non-polymers45214
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)37.148, 49.031, 49.053
Angle α, β, γ (deg.)69.75, 69.08, 77.56
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein BETA_LACTOGLOBULIN-1/B / BETA-LACTOGLOBULIN- A AND B VARIANTOF BETA-LG


Mass: 18197.113 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: NATURAL VARIANTS A AND B IN RATIO 60-40 / Source: (natural) OVIS ARIES (sheep) / Variant: B AND C IN 50 PERCENT RATIO / Tissue: MILK / References: UniProt: P67976

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Non-polymers , 6 types, 503 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-NH4 / AMMONIUM ION


Mass: 18.038 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: H4N
#4: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 476 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsNATURAL VARIANTS B RESIDUE 20 HIS AND A RESIDUE 20 TYR ARE PRESENT IN CRYSTAL STRUCTURE

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.15 Å3/Da / Density % sol: 42.7 % / Description: NONE
Crystal growpH: 5.6
Details: 0.2M SODIUM CITRATE, 0.1M SODIUM POTASSIUM TARTRATE, 2.0M AMMONIUM SULPHATE, PH 5.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.2 / Wavelength: 0.932
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 11, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.932 Å / Relative weight: 1
ReflectionResolution: 1.12→15 Å / Num. obs: 116059 / % possible obs: 92.3 % / Observed criterion σ(I): 3 / Redundancy: 4 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 9.4
Reflection shellResolution: 1.12→1.14 Å / Rmerge(I) obs: 1.23 / Mean I/σ(I) obs: 3.7 / % possible all: 89.4

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
DENZOdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GXA

1gxa


Resolution: 1.12→14.7 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.971 / SU B: 1.108 / SU ML: 0.024 / Cross valid method: THROUGHOUT / ESU R: 0.035 / ESU R Free: 0.036 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY THE N-TERMINAL RESIDUE 1-4 OF CHAIN A IS A MOBILE REGION WHICH HAS BEEN DIFFICULT TO MODEL SATISFACTORILY THE ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY THE N-TERMINAL RESIDUE 1-4 OF CHAIN A IS A MOBILE REGION WHICH HAS BEEN DIFFICULT TO MODEL SATISFACTORILY THE REGION 61-65 IS A MOBILE LOOP WHICH HAS BEEN DIFFICULT TO MODEL SATISFACTORILY
RfactorNum. reflection% reflectionSelection details
Rfree0.16942 5364 5 %RANDOM
Rwork0.13926 ---
obs0.14078 101671 92.23 %-
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 mean: 16.567 Å2
Baniso -1Baniso -2Baniso -3
1-0.51 Å2-0.09 Å20.92 Å2
2--0.65 Å20.48 Å2
3----0.56 Å2
Refinement stepCycle: LAST / Resolution: 1.12→14.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2542 0 47 476 3065
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.022863
X-RAY DIFFRACTIONr_bond_other_d0.0010.022863
X-RAY DIFFRACTIONr_angle_refined_deg1.92623897
X-RAY DIFFRACTIONr_angle_other_deg1.47836703
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3495365
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.77726.719128
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.63115600
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.06157
X-RAY DIFFRACTIONr_chiral_restr0.3320.2449
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0213152
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02555
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr13.67535726
X-RAY DIFFRACTIONr_sphericity_free31.91853
X-RAY DIFFRACTIONr_sphericity_bonded16.21456167
LS refinement shellResolution: 1.12→1.149 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.214 373 -
Rwork0.18 7274 -
obs--89.65 %

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