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- PDB-1ova: CRYSTAL STRUCTURE OF UNCLEAVED OVALBUMIN AT 1.95 ANGSTROMS RESOLUTION -

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Basic information

Entry
Database: PDB / ID: 1ova
TitleCRYSTAL STRUCTURE OF UNCLEAVED OVALBUMIN AT 1.95 ANGSTROMS RESOLUTION
Components(OVALBUMIN) x 3
KeywordsSERPIN
Function / homology
Function and homology information


intracellular amino acid homeostasis / RUNX1 regulates transcription of genes involved in differentiation of keratinocytes / phagolysosome / monoatomic ion homeostasis / embryo development ending in birth or egg hatching / response to steroid hormone / response to corticosterone / phagocytic vesicle / monoatomic ion transport / early endosome lumen ...intracellular amino acid homeostasis / RUNX1 regulates transcription of genes involved in differentiation of keratinocytes / phagolysosome / monoatomic ion homeostasis / embryo development ending in birth or egg hatching / response to steroid hormone / response to corticosterone / phagocytic vesicle / monoatomic ion transport / early endosome lumen / Neutrophil degranulation / response to progesterone / response to estrogen / protease binding / vesicle / intracellular membrane-bounded organelle / calcium ion binding / endoplasmic reticulum / extracellular space / extracellular region / cytosol
Similarity search - Function
Antithrombin; Chain I, domain 2 / Antithrombin, subunit I, domain 2 / Alpha-1-antitrypsin; domain 1 / Alpha-1-antitrypsin, domain 1 / Serpin, conserved site / Serpins signature. / Serpin superfamily, domain 2 / Serpin family / Serpin domain / Serpin superfamily ...Antithrombin; Chain I, domain 2 / Antithrombin, subunit I, domain 2 / Alpha-1-antitrypsin; domain 1 / Alpha-1-antitrypsin, domain 1 / Serpin, conserved site / Serpins signature. / Serpin superfamily, domain 2 / Serpin family / Serpin domain / Serpin superfamily / Serpin superfamily, domain 1 / Serpin (serine protease inhibitor) / SERine Proteinase INhibitors / Roll / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / Resolution: 1.95 Å
AuthorsStein, P.E. / Leslie, A.G.W.
Citation
Journal: J.Mol.Biol. / Year: 1991
Title: Crystal structure of uncleaved ovalbumin at 1.95 A resolution.
Authors: Stein, P.E. / Leslie, A.G. / Finch, J.T. / Carrell, R.W.
#1: Journal: Nature / Year: 1990
Title: Crystal Structure of Ovalbumin as a Model for the Reactive Centre of Serpins
Authors: Stein, P.E. / Leslie, A.G.W. / Finch, J.T. / Turnell, W.G. / Mclaughlin, P.J. / Carrell, R.W.
History
DepositionNov 26, 1990Processing site: BNL
Revision 1.0Apr 15, 1992Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.process_site / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_PDB_ins_code / _struct_conn.pdbx_ptnr2_PDB_ins_code / _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 / _struct_conn.ptnr2_symmetry
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: OVALBUMIN
B: OVALBUMIN
C: OVALBUMIN
D: OVALBUMIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)172,4379
Polymers171,5124
Non-polymers9255
Water12,214678
1
A: OVALBUMIN
B: OVALBUMIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,3585
Polymers85,8762
Non-polymers4823
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: OVALBUMIN
D: OVALBUMIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,0784
Polymers85,6362
Non-polymers4422
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.900, 84.700, 71.500
Angle α, β, γ (deg.)87.50, 104.00, 108.50
Int Tables number1
Space group name H-MP1
Atom site foot note1: RESIDUES SER A 87C, SER A 350 AND SER B 350 ARE PHOSHORYLATED.
2: THERE IS A GLYCOSIDIC BOND BETWEEN ND2 OF ASN 298 AND C1 OF NAG OF EACH CHAIN.
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.74109, -0.67004, 0.04278), (-0.67054, 0.7354, -0.0978), (0.03407, -0.10116, -0.99429)35.49, 18.48, 80.6
2given(0.99403, -0.06828, -0.08507), (0.07993, 0.98662, 0.14209), (0.07423, -0.14804, 0.98619)23.07, -42.91, 9.15
3given(-0.81974, -0.57173, 0.03395), (-0.57273, 0.818, -0.0534), (0.00276, -0.06322, -0.998)43.03, -26.65, 84.39
4given(-0.78775, -0.61599, 0.00134), (-0.61475, 0.7863, 0.06169), (-0.03906, 0.04777, -0.99809)47.94, -29.6, 76.52
5given(0.99165, -0.12686, -0.02319), (0.1277, 0.99103, 0.03933), (0.0181, -0.04196, 0.99896)24.79, -38.65, 0.99
6given(-0.86039, -0.50766, -0.04482), (-0.50956, 0.85541, 0.09287), (-0.00881, 0.10274, -0.99467)26.75, 3.54, 74.8
DetailsTHE TRANSFORMATION PRESENTED IN THE *MTRIX 1* RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAIN *A* WHEN APPLIED TO CHAIN *B*. THE TRANSFORMATION PRESENTED IN THE *MTRIX 2* RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAIN *A* WHEN APPLIED TO CHAIN *C*. THE TRANSFORMATION PRESENTED IN THE *MTRIX 3* RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAIN *A* WHEN APPLIED TO CHAIN *D*. THE TRANSFORMATION PRESENTED IN THE *MTRIX 4* RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAIN *B* WHEN APPLIED TO CHAIN *C*. THE TRANSFORMATION PRESENTED IN THE *MTRIX 5* RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAIN *B* WHEN APPLIED TO CHAIN *D*. THE TRANSFORMATION PRESENTED IN THE *MTRIX 6* RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAIN *C* WHEN APPLIED TO CHAIN *D*.

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Components

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Protein , 3 types, 4 molecules ABCD

#1: Protein OVALBUMIN


Mass: 42977.906 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / References: UniProt: P01012
#2: Protein OVALBUMIN


Mass: 42897.930 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / References: UniProt: P01012
#3: Protein OVALBUMIN


Mass: 42817.953 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / References: UniProt: P01012

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Sugars , 1 types, 4 molecules

#4: 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.: 4 / Source method: obtained synthetically / 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 , 2 types, 679 molecules

#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 678 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.04 Å3/Da / Density % sol: 39.77 %
Crystal grow
*PLUS
Temperature: 37 ℃ / pH: 6.4 / Method: batch method
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
125 mg/mlprotein11
250 %satammonium sulfate11
350 mMcacodylate11

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 2.7 Å / Num. obs: 94362 / % possible obs: 94 % / Num. measured all: 352293 / Rmerge(I) obs: 0.052

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementRfactor obs: 0.169 / Highest resolution: 1.95 Å
Refinement stepCycle: LAST / Highest resolution: 1.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11534 0 57 678 12269
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.020.02
X-RAY DIFFRACTIONp_angle_d0.040.03
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.060.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it8.32
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it13.23
X-RAY DIFFRACTIONp_scangle_it16.34
X-RAY DIFFRACTIONp_plane_restr0.010.02
X-RAY DIFFRACTIONp_chiral_restr0.190.15
X-RAY DIFFRACTIONp_singtor_nbd0.160.2
X-RAY DIFFRACTIONp_multtor_nbd0.170.2
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor17.315
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor

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