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- PDB-3qkg: Crystal structure of alpha-1-microglobulin at 2.3 A resolution -

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Basic information

Entry
Database: PDB / ID: 3qkg
TitleCrystal structure of alpha-1-microglobulin at 2.3 A resolution
ComponentsProtein AMBP
KeywordsIMMUNE SYSTEM / Beta barrel / binding protein / Bound chromophore / Human plasma
Function / homology
Function and homology information


Oxidoreductases; Acting on NADH or NADPH; With a heme protein as acceptor / calcium oxalate binding / IgA binding / heme catabolic process / negative regulation of immune response / negative regulation of JNK cascade / calcium channel inhibitor activity / Scavenging of heme from plasma / female pregnancy / serine-type endopeptidase inhibitor activity ...Oxidoreductases; Acting on NADH or NADPH; With a heme protein as acceptor / calcium oxalate binding / IgA binding / heme catabolic process / negative regulation of immune response / negative regulation of JNK cascade / calcium channel inhibitor activity / Scavenging of heme from plasma / female pregnancy / serine-type endopeptidase inhibitor activity / carbohydrate binding / nuclear membrane / collagen-containing extracellular matrix / mitochondrial inner membrane / blood microparticle / oxidoreductase activity / cell adhesion / heme binding / cell surface / endoplasmic reticulum / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / plasma membrane / cytosol
Similarity search - Function
Protein AMBP / Alpha-1-microglobulin / Lipocalin family conserved site / Proteinase inhibitor I2, Kunitz, conserved site / Pancreatic trypsin inhibitor (Kunitz) family signature. / BPTI/Kunitz family of serine protease inhibitors. / Pancreatic trypsin inhibitor Kunitz domain / Kunitz/Bovine pancreatic trypsin inhibitor domain / Pancreatic trypsin inhibitor (Kunitz) family profile. / Pancreatic trypsin inhibitor Kunitz domain superfamily ...Protein AMBP / Alpha-1-microglobulin / Lipocalin family conserved site / Proteinase inhibitor I2, Kunitz, conserved site / Pancreatic trypsin inhibitor (Kunitz) family signature. / BPTI/Kunitz family of serine protease inhibitors. / Pancreatic trypsin inhibitor Kunitz domain / Kunitz/Bovine pancreatic trypsin inhibitor domain / Pancreatic trypsin inhibitor (Kunitz) family profile. / Pancreatic trypsin inhibitor Kunitz domain superfamily / 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
NICKEL (II) ION / Protein AMBP
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsMeining, W. / Skerra, A.
CitationJournal: Biochem.J. / Year: 2012
Title: The crystal structure of human alpha(1)-microglobulin reveals a potential haem-binding site.
Authors: Meining, W. / Skerra, A.
History
DepositionFeb 1, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 8, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 20, 2012Group: Database references
Revision 1.2Jun 19, 2013Group: Database references
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein AMBP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,1083
Polymers21,9571
Non-polymers1512
Water84747
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.721, 66.721, 80.255
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Protein AMBP / Alpha-1-microglobulin / Protein HC / Alpha-1 microglycoprotein / Complex-forming glycoprotein ...Alpha-1-microglobulin / Protein HC / Alpha-1 microglycoprotein / Complex-forming glycoprotein heterogeneous in charge / Inter-alpha-trypsin inhibitor light chain / ITI-LC / Bikunin / EDC1 / HI-30 / Uronic-acid-rich protein / Trypstatin


Mass: 21956.834 Da / Num. of mol.: 1 / Fragment: lipocalin / Mutation: C34S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AMBP, HCP, ITIL / Plasmid: pa1m2 / Production host: Escherichia coli (E. coli) / Strain (production host): K-12 / References: UniProt: P02760
#2: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 47 / 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: 2.32 Å3/Da / Density % sol: 47.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 100 mM Tris-HCl, 1.1 M sodium citrate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 105 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 29, 2011
RadiationMonochromator: Si-111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.17→46.89 Å / Num. obs: 10877 / % possible obs: 96.5 % / Observed criterion σ(F): 2.5 / Redundancy: 10.4 % / Rmerge(I) obs: 0.073
Reflection shellResolution: 2.17→2.29 Å / Redundancy: 7.3 % / Rmerge(I) obs: 1.38 / % possible all: 80

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
MrBUMPphasing
REFMAC5.5.0109refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→46.89 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.94 / SU B: 19.515 / SU ML: 0.224 / Cross valid method: THROUGHOUT / ESU R: 0.309 / ESU R Free: 0.237 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25952 452 4.8 %RANDOM
Rwork0.2126 ---
obs0.21478 9044 99.33 %-
all-8341 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 71.936 Å2
Baniso -1Baniso -2Baniso -3
1--2.35 Å2-1.17 Å20 Å2
2---2.35 Å20 Å2
3---3.52 Å2
Refinement stepCycle: LAST / Resolution: 2.3→46.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1317 0 7 47 1371
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0221353
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7031.9411829
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4475163
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.58523.54862
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.91315237
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.331159
X-RAY DIFFRACTIONr_chiral_restr0.1140.2199
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211011
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.8961.5812
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.67421316
X-RAY DIFFRACTIONr_scbond_it2.7083541
X-RAY DIFFRACTIONr_scangle_it4.4284.5513
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.485 31 -
Rwork0.34 655 -
obs--98.85 %
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)
16.73472.4013-0.71326.05691.17436.7829-0.43770.294-0.21030.10320.2054-0.05320.23470.3580.23230.5226-0.0737-0.00080.31160.03410.0604-18.10316.985-1.288
21.34492.55676.53784.0462-6.08375.0214-0.0763-0.5462-0.36881.3359-0.0883-0.14710.09930.37150.16461.6242-0.065-0.0420.93070.02220.4704-15.82112.53212.042
32.31282.9719-1.18216.0564-0.87512.16140.0077-0.11020.01790.36470.0516-0.0337-0.05950.1959-0.05930.5163-0.0848-0.0110.45120.00790.0725-22.46615.2974.024
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A8 - 34
2X-RAY DIFFRACTION2A35 - 79
3X-RAY DIFFRACTION3A80 - 171

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