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- PDB-1bik: X-RAY STRUCTURE OF BIKUNIN FROM THE HUMAN INTER-ALPHA-INHIBITOR C... -

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Basic information

Entry
Database: PDB / ID: 1bik
TitleX-RAY STRUCTURE OF BIKUNIN FROM THE HUMAN INTER-ALPHA-INHIBITOR COMPLEX
ComponentsBIKUNIN
KeywordsGLYCOPROTEIN / BIKUNIN / TRYPSTATIN / URINARY TRYPSIN INHIBITOR / URONIC-ACID-RICH PROTEIN / SERINE PROTEASE INHIBITOR (KUNITZ TYPE) / GLYCOSYLATED PROTEIN
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 / Pancreatic trypsin inhibitor Kunitz domain / Factor Xa Inhibitor / 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 ...Protein AMBP / Alpha-1-microglobulin / Pancreatic trypsin inhibitor Kunitz domain / Factor Xa Inhibitor / 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 / Few Secondary Structures / Irregular / Lipocalin signature.
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsXu, Y. / Carr, P.D. / Guss, J.M. / Ollis, D.L.
CitationJournal: J.Mol.Biol. / Year: 1998
Title: The crystal structure of bikunin from the inter-alpha-inhibitor complex: a serine protease inhibitor with two Kunitz domains.
Authors: Xu, Y. / Carr, P.D. / Guss, J.M. / Ollis, D.L.
History
DepositionNov 26, 1997Processing site: BNL
Revision 1.0Mar 16, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Jul 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_leaving_atom_flag / _struct_conn.pdbx_role / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Aug 2, 2023Group: Database references / Refinement description / Structure summary
Category: chem_comp / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Nov 20, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BIKUNIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,4004
Polymers15,9871
Non-polymers4133
Water59433
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.300, 55.300, 146.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein BIKUNIN / MINGIN / URINARY TRYPSIN INHIBITOR / HI30 / TRYPSTATIN


Mass: 15987.002 Da / Num. of mol.: 1 / Fragment: DOMAIN II,78 - 133 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Secretion: URINE / References: UniProt: P02760
#2: 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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
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
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / 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: 3.51 Å3/Da / Density % sol: 64.97 %
Description: NON IDENTICAL RESIDUES TRUNCATED TO THE CB POSITION
Crystal growpH: 7.5 / Details: pH 7.5
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 mg/mlprotein1drop
22 Mammonium sulfate1drop
34 %PEG4001drop
40.1 MHEPES1drop

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Nov 1, 1995 / Details: COLLIMATOR
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→25 Å / Num. obs: 8519 / % possible obs: 97.7 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 13.4
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 6 % / Rmerge(I) obs: 0.21 / Mean I/σ(I) obs: 10.1 / % possible all: 97.6
Reflection
*PLUS
Num. measured all: 55165
Reflection shell
*PLUS
% possible obs: 97.6 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: C-TERMINAL DOMAIN OF PDB ENTRY 1KNT

1knt


Resolution: 2.5→8 Å / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.253 783 10 %RANDOM
Rwork0.205 ---
obs0.205 7511 89 %-
Refinement stepCycle: LAST / Resolution: 2.5→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms827 0 24 33 884
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
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_deg1.635
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.25
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.389
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2.5→2.6 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.305 98 10 %
Rwork0.29 696 -
obs--79 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2WATER.PARMWATER.TOPO
X-RAY DIFFRACTION3SO4.PARMSO4.TOPO
X-RAY DIFFRACTION4GLA_NEW.TOPO
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.25
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.389
LS refinement shell
*PLUS
Rfactor obs: 0.29

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