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- PDB-4es7: crystal structure of protein HC from Homo sapiens at 2 angstrom -

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Basic information

Entry
Database: PDB / ID: 4es7
Titlecrystal structure of protein HC from Homo sapiens at 2 angstrom
ComponentsProtein AMBP
KeywordsIMMUNE SYSTEM
Function / homology
Function and homology information


Oxidoreductases; Acting on NADH or NADPH; With a heme protein as acceptor / calcium oxalate binding / IgA binding / negative regulation of immune response / heme catabolic process / negative regulation of JNK cascade / Scavenging of heme from plasma / calcium channel inhibitor activity / protein catabolic process / serine-type endopeptidase inhibitor activity ...Oxidoreductases; Acting on NADH or NADPH; With a heme protein as acceptor / calcium oxalate binding / IgA binding / negative regulation of immune response / heme catabolic process / negative regulation of JNK cascade / Scavenging of heme from plasma / calcium channel inhibitor activity / protein catabolic process / serine-type endopeptidase inhibitor activity / female pregnancy / : / carbohydrate binding / nuclear membrane / blood microparticle / oxidoreductase activity / cell adhesion / mitochondrial inner membrane / 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 / Lipocalin / cytosolic fatty-acid binding protein family / Lipocalin/cytosolic fatty-acid binding domain / Calycin beta-barrel core domain / Calycin / Lipocalin / Lipocalin signature. / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Protein AMBP
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.001 Å
AuthorsZhang, Y.L. / Gao, Z.Q. / Wang, D.Q. / Dong, Y.H.
CitationJournal: To be Published
Title: crystal structure of protein HC from Home sapiens at 2 angstrom
Authors: Zhang, Y.L. / Gao, Z.Q. / Wang, D.Q. / Dong, Y.H.
History
DepositionApr 22, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 24, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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

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Assembly

Deposited unit
A: Protein AMBP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,9524
Polymers22,6341
Non-polymers3183
Water97354
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)36.437, 36.437, 112.667
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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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: 22633.561 Da / Num. of mol.: 1 / Fragment: UNP residues 27-193
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AMBP, HCP, ITIL / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / References: UniProt: P02760
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 54 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.95 Å3/Da / Density % sol: 36.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.9
Details: 0.2M ammonium citrate, 20% PEG 3350, 0.1M HEPES pH 6.9, 40% 1,1,1,3,3,3-Hexafluoro-z-propanol, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 20, 2011
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 9932 / Num. obs: 9932 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.1 % / Biso Wilson estimate: 30.63 Å2 / Rmerge(I) obs: 0.076 / Net I/σ(I): 50.3
Reflection shellResolution: 2→2.07 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.383 / Mean I/σ(I) obs: 8.57 / Num. unique all: 982 / % possible all: 100

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.001→34.669 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.12 / σ(F): 1.34 / Phase error: 28.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2611 475 4.81 %RANDOM
Rwork0.1987 ---
all0.2019 9932 --
obs0.2019 9867 99.64 %-
Solvent computationShrinkage radii: 0.6 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.087 Å2 / ksol: 0.379 e/Å3
Displacement parametersBiso max: 93.44 Å2 / Biso mean: 40.3096 Å2 / Biso min: 15.56 Å2
Baniso -1Baniso -2Baniso -3
1-0.8994 Å20 Å2-0 Å2
2--0.8994 Å20 Å2
3----1.7987 Å2
Refinement stepCycle: LAST / Resolution: 2.001→34.669 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1331 0 21 54 1406
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071380
X-RAY DIFFRACTIONf_angle_d1.2341855
X-RAY DIFFRACTIONf_dihedral_angle_d16.074512
X-RAY DIFFRACTIONf_chiral_restr0.083200
X-RAY DIFFRACTIONf_plane_restr0.004233
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 3

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.0007-2.29010.2821580.2154309699
2.2901-2.88510.33421530.21143152100
2.8851-34.67420.23291640.19053144100
Refinement TLS params.Method: refined / Origin x: 14.9191 Å / Origin y: -6.7183 Å / Origin z: -9.2317 Å
111213212223313233
T0.0463 Å20.0332 Å2-0.0247 Å2-0.0306 Å20.0117 Å2--0.0349 Å2
L1.9292 °20.334 °20.2871 °2-1.0971 °20.172 °2--2.2438 °2
S-0.0045 Å °-0.0145 Å °-0.1327 Å °-0.0135 Å °0.029 Å °0.0613 Å °0.0716 Å °0.0645 Å °-0.0156 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA2 - 167
2X-RAY DIFFRACTION1allA301 - 354
3X-RAY DIFFRACTION1allA201 - 203

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