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- PDB-4oik: (Quasi-)Racemic X-ray crystal structure of glycosylated chemokine... -

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Basic information

Entry
Database: PDB / ID: 4oik
Title(Quasi-)Racemic X-ray crystal structure of glycosylated chemokine Ser-CCL1.
Components
  • C-C motif chemokine 1Chemokine
  • D-Ser-CCL1
KeywordsSIGNALING PROTEIN / Chemical protein synthesis / quasi-racemic protein crystallography / Glycoprotein / Chemokine
Function / homology
Function and homology information


CCR chemokine receptor binding / lymphocyte chemotaxis / eosinophil chemotaxis / chemokine-mediated signaling pathway / positive regulation of monocyte chemotaxis / Chemokine receptors bind chemokines / chemokine activity / positive regulation of interleukin-17 production / monocyte chemotaxis / cellular response to interleukin-1 ...CCR chemokine receptor binding / lymphocyte chemotaxis / eosinophil chemotaxis / chemokine-mediated signaling pathway / positive regulation of monocyte chemotaxis / Chemokine receptors bind chemokines / chemokine activity / positive regulation of interleukin-17 production / monocyte chemotaxis / cellular response to interleukin-1 / viral process / neutrophil chemotaxis / cellular response to type II interferon / positive regulation of inflammatory response / intracellular calcium ion homeostasis / chemotaxis / cellular response to tumor necrosis factor / G alpha (i) signalling events / positive regulation of cytosolic calcium ion concentration / positive regulation of ERK1 and ERK2 cascade / inflammatory response / G protein-coupled receptor signaling pathway / signal transduction / extracellular space / extracellular region
Similarity search - Function
CC chemokine, conserved site / Small cytokines (intercrine/chemokine) C-C subfamily signature. / Chemokine beta/gamma/delta / Intercrine alpha family (small cytokine C-X-C) (chemokine CXC). / Chemokine interleukin-8-like domain / Chemokine interleukin-8-like superfamily / Small cytokines (intecrine/chemokine), interleukin-8 like / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #40 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
CITRIC ACID / polypeptide(D) / polypeptide(D) (> 10) / C-C motif chemokine 1
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsOkamoto, R. / Mandal, K. / Sawaya, M.R. / Kajihara, Y. / Yeates, T.O. / Kent, S.B.H.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2014
Title: (Quasi-)Racemic X-ray Structures of Glycosylated and Non-Glycosylated Forms of the Chemokine Ser-CCL1 Prepared by Total Chemical Synthesis.
Authors: Okamoto, R. / Mandal, K. / Sawaya, M.R. / Kajihara, Y. / Yeates, T.O. / Kent, S.B.
History
DepositionJan 19, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 7, 2014Provider: repository / Type: Initial release
Revision 1.1May 21, 2014Group: Database references
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_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_asym_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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
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

Downloads & links

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Assembly

Deposited unit
A: C-C motif chemokine 1
B: C-C motif chemokine 1
C: D-Ser-CCL1
D: D-Ser-CCL1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,78335
Polymers34,3634
Non-polymers3,42031
Water2,018112
1
A: C-C motif chemokine 1
B: C-C motif chemokine 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,07219
Polymers17,1882
Non-polymers1,88317
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2130 Å2
ΔGint-22 kcal/mol
Surface area9750 Å2
MethodPISA
2
C: D-Ser-CCL1
D: D-Ser-CCL1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,71116
Polymers17,1742
Non-polymers1,53714
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1600 Å2
ΔGint-16 kcal/mol
Surface area9540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.410, 51.680, 51.330
Angle α, β, γ (deg.)111.23, 106.33, 108.68
Int Tables number1
Space group name H-MP1

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Components

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Protein , 2 types, 4 molecules ABCD

#1: Protein C-C motif chemokine 1 / Chemokine / Small-inducible cytokine A1 / T lymphocyte-secreted protein I-309


Mass: 8594.190 Da / Num. of mol.: 2 / Fragment: UNP residues 23-96 / Source method: obtained synthetically / Source: (gene. exp.) Homo sapiens (human) / References: UniProt: P22362
#2: Protein D-Ser-CCL1


Mass: 8587.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Chemical Synthesis / Source: (synth.) synthetic construct (others)

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Sugars , 1 types, 2 molecules

#3: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 141 molecules

#4: Chemical...
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 27 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 112 / 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: 2.76 Å3/Da / Density % sol: 55.51 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 3.5
Details: 2 M Ammonium Sulfate, 0.1 M citric acid, pH 3.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97921 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 8, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97921 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 16903 / Num. obs: 16903 / % possible obs: 75.3 % / Redundancy: 3.7 % / Biso Wilson estimate: 24.16 Å2 / Rmerge(I) obs: 0.164 / Net I/σ(I): 6.3
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 1.4 % / Rmerge(I) obs: 0.416 / Mean I/σ(I) obs: 2.1 / Num. unique all: 313 / % possible all: 13.9

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Processing

Software
NameVersionClassification
PHASERphasing
BUSTER2.8.0refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4OIJ

4oij


Resolution: 2.1→39.12 Å / Cor.coef. Fo:Fc: 0.9281 / Cor.coef. Fo:Fc free: 0.9084 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2758 850 5.05 %RANDOM
Rwork0.2285 ---
obs0.2309 16816 --
Displacement parametersBiso mean: 67.41 Å2
Baniso -1Baniso -2Baniso -3
1-11.6612 Å2-3.1424 Å2-1.1654 Å2
2---21.2756 Å21.4014 Å2
3---9.6145 Å2
Refine analyzeLuzzati coordinate error obs: 0.445 Å
Refinement stepCycle: LAST / Resolution: 2.1→39.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2318 0 189 112 2619
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012536HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.173418HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d636SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes42HARMONIC2
X-RAY DIFFRACTIONt_gen_planes358HARMONIC5
X-RAY DIFFRACTIONt_it2512HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.97
X-RAY DIFFRACTIONt_other_torsion20.31
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion308SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2431SEMIHARMONIC4
LS refinement shellResolution: 2.1→2.22 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.2164 34 4.02 %
Rwork0.2098 811 -
all0.2101 845 -
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)
110.6312-3.6185-0.76633.7309-2.61745.4829-0.395-0.6799-0.81220.37620.0180.14050.52910.30560.377-0.1282-0.02340.04130.00290.1075-0.26984.06814.064132.4486
211.5271-3.9035-0.15474.0452.31515.2306-0.4093-0.75390.88320.4141-0.0668-0.1087-0.5821-0.31450.4761-0.1576-0.0259-0.04020.0649-0.1426-0.2806-11.947119.036932.442
312.5562-3.6354-0.08124.3907-2.52828.02740.33070.67260.7462-0.12740.1119-0.0026-0.4324-0.6976-0.4426-0.2214-0.01970.047-0.03070.1475-0.2129.756419.406211.0235
412.3864-3.04551.60244.40222.74247.75340.22970.8809-0.7011-0.09690.10070.08080.36030.684-0.3304-0.2106-0.0181-0.018-0.0385-0.1575-0.249427.6093.732210.7926
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|1 - A|73 A|101 - A|101 }A1 - 73
2X-RAY DIFFRACTION1{ A|1 - A|73 A|101 - A|101 }A101
3X-RAY DIFFRACTION2{ B|1 - B|73 B|101 - B|101 }B1 - 73
4X-RAY DIFFRACTION2{ B|1 - B|73 B|101 - B|101 }B101
5X-RAY DIFFRACTION3{ C|3 - C|57 C|58 - C|73 }C3 - 57
6X-RAY DIFFRACTION3{ C|3 - C|57 C|58 - C|73 }C58 - 73
7X-RAY DIFFRACTION4{ D|3 - D|57 D|58 - D|73 }D3 - 57
8X-RAY DIFFRACTION4{ D|3 - D|57 D|58 - D|73 }D58 - 73

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