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- PDB-1mr8: MIGRATION INHIBITORY FACTOR-RELATED PROTEIN 8 FROM HUMAN -

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Basic information

Entry
Database: PDB / ID: 1mr8
TitleMIGRATION INHIBITORY FACTOR-RELATED PROTEIN 8 FROM HUMAN
ComponentsMIGRATION INHIBITORY FACTOR-RELATED PROTEIN 8
KeywordsMETAL TRANSPORT / CALCIUM-BINDING PROTEIN / MAD / MIGRATION INHIBITORY FACTOR_ RELATED PROTEIN 8 / S100 PROTEIN
Function / homology
Function and homology information


sequestering of zinc ion / calprotectin complex / neutrophil aggregation / positive regulation of peptide secretion / autocrine signaling / Toll-like receptor 4 binding / chronic inflammatory response / Metal sequestration by antimicrobial proteins / peptide secretion / leukocyte migration involved in inflammatory response ...sequestering of zinc ion / calprotectin complex / neutrophil aggregation / positive regulation of peptide secretion / autocrine signaling / Toll-like receptor 4 binding / chronic inflammatory response / Metal sequestration by antimicrobial proteins / peptide secretion / leukocyte migration involved in inflammatory response / RAGE receptor binding / Regulation of TLR by endogenous ligand / astrocyte development / MyD88 deficiency (TLR2/4) / arachidonic acid binding / intermediate filament cytoskeleton / IRAK4 deficiency (TLR2/4) / MyD88:MAL(TIRAP) cascade initiated on plasma membrane / regulation of toll-like receptor signaling pathway / response to zinc ion / regulation of cytoskeleton organization / peptidyl-cysteine S-nitrosylation / RHO GTPases Activate NADPH Oxidases / defense response to fungus / positive regulation of intrinsic apoptotic signaling pathway / neutrophil chemotaxis / autophagy / positive regulation of inflammatory response / calcium-dependent protein binding / activation of cysteine-type endopeptidase activity involved in apoptotic process / positive regulation of NF-kappaB transcription factor activity / ER-Phagosome pathway / positive regulation of cell growth / microtubule binding / secretory granule lumen / response to ethanol / collagen-containing extracellular matrix / response to lipopolysaccharide / cytoskeleton / defense response to bacterium / inflammatory response / innate immune response / apoptotic process / calcium ion binding / Neutrophil degranulation / extracellular space / zinc ion binding / extracellular exosome / extracellular region / nucleus / plasma membrane / cytosol
Similarity search - Function
S-100/ICaBP type calcium binding protein signature. / S100/Calcium binding protein 7/8-like, conserved site / S100/CaBP-9k-type, calcium binding, subdomain / S-100/ICaBP type calcium binding domain / S-100/ICaBP type calcium binding domain / EF-hand / Recoverin; domain 1 / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. ...S-100/ICaBP type calcium binding protein signature. / S100/Calcium binding protein 7/8-like, conserved site / S100/CaBP-9k-type, calcium binding, subdomain / S-100/ICaBP type calcium binding domain / S-100/ICaBP type calcium binding domain / EF-hand / Recoverin; domain 1 / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å
AuthorsIshikawa, K. / Nakagawa, A. / Tanaka, I. / Nishihira, J.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2000
Title: The structure of human MRP8, a member of the S100 calcium-binding protein family, by MAD phasing at 1.9 A resolution.
Authors: Ishikawa, K. / Nakagawa, A. / Tanaka, I. / Suzuki, M. / Nishihira, J.
History
DepositionApr 13, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0May 17, 2000Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _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_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: MIGRATION INHIBITORY FACTOR-RELATED PROTEIN 8
B: MIGRATION INHIBITORY FACTOR-RELATED PROTEIN 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,8676
Polymers21,7072
Non-polymers1604
Water1,856103
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2930 Å2
ΔGint-80 kcal/mol
Surface area9860 Å2
MethodPISA
2
A: MIGRATION INHIBITORY FACTOR-RELATED PROTEIN 8
B: MIGRATION INHIBITORY FACTOR-RELATED PROTEIN 8
hetero molecules

A: MIGRATION INHIBITORY FACTOR-RELATED PROTEIN 8
B: MIGRATION INHIBITORY FACTOR-RELATED PROTEIN 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,73512
Polymers43,4144
Non-polymers3218
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+2/31
Buried area7790 Å2
ΔGint-176 kcal/mol
Surface area17780 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)52.500, 52.500, 128.600
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.910629, 0.412598, -0.022762), (0.409931, 0.895053, -0.175603), (-0.05208, -0.16924, -0.984198)
Vector: 34.756, -0.062, 74.858)

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Components

#1: Protein MIGRATION INHIBITORY FACTOR-RELATED PROTEIN 8 / MRP8 / S100A8 / CALGRANULIN A


Mass: 10853.528 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell: LYMPHOCYTE / Tissue: BLOOD / References: UniProt: P05109
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 103 / 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: 2.36 Å3/Da / Density % sol: 48 %
Description: INITIAL DENSITY WAS OBTAINED BY THE MAD USING YTTERBIUM DERIVATIVE, THEN REFINED NATIVE STRUCUURE
Crystal growpH: 6.2
Details: 15%(W/V) PEG6000, 0.1M MES, 0.1M MES PH 6.2, 20MM CACL2
Crystal grow
*PLUS
Temperature: 291 K / pH: 6 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
215 %(w/v)PEG60001reservoir
37 %(v/v)MPD1reservoir
40.1 MMES1reservoir
520 mM1reservoirCaCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6B / Wavelength: 1
DetectorType: FUJI / Detector: IMAGE PLATE / Date: Jan 1, 1995 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→37 Å / Num. obs: 97834 / % possible obs: 96.3 % / Redundancy: 6 % / Biso Wilson estimate: 12.9 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 10.1
Reflection shellResolution: 1.9→2 Å / Redundancy: 5 % / Rmerge(I) obs: 0.334 / Mean I/σ(I) obs: 2.1 / % possible all: 96.3
Reflection
*PLUS
Num. obs: 16285 / Num. measured all: 97834
Reflection shell
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 2 Å / % possible obs: 88.5 % / Num. unique obs: 2129 / Num. measured obs: 10549

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Processing

Software
NameVersionClassification
SHARPphasing
X-PLOR3.851refinement
DENZOdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MAD / Resolution: 1.9→20 Å / Rfactor Rfree error: 0.006 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.234 1602 10.1 %RANDOM
Rwork0.193 ---
obs0.193 15822 93.9 %-
Displacement parametersBiso mean: 26.2 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.23 Å0.22 Å
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1470 0 4 103 1577
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.005
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23.8
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.63
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.951.5
X-RAY DIFFRACTIONx_mcangle_it3.132
X-RAY DIFFRACTIONx_scbond_it3.772
X-RAY DIFFRACTIONx_scangle_it6.042.5
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.29 235 10.1 %
Rwork0.266 2093 -
obs--84.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAMETER.ELEMENTSTOPOLOGY.ELEMENTS
X-RAY DIFFRACTION3WATER.TOP
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 20 Å / σ(F): 0 / % reflection Rfree: 10.1 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 26.2 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_angle_deg1
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.8
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.63
X-RAY DIFFRACTIONx_mcbond_it1.5
X-RAY DIFFRACTIONx_scbond_it2
X-RAY DIFFRACTIONx_mcangle_it2
X-RAY DIFFRACTIONx_scangle_it2.5
LS refinement shell
*PLUS
Highest resolution: 1.9 Å / Rfactor Rfree: 0.29 / % reflection Rfree: 10.1 % / Rfactor Rwork: 0.266

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