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- PDB-2vh4: Structure of a loop C-sheet serpin polymer -

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Basic information

Entry
Database: PDB / ID: 2vh4
TitleStructure of a loop C-sheet serpin polymer
ComponentsTENGPIN
KeywordsHYDROLASE INHIBITOR / SERPIN / C SHEET POLYMER / LATENT CONFORMATION
Function / homology
Function and homology information


serine-type endopeptidase inhibitor activity / extracellular space
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
Serine protease inhibitor
Similarity search - Component
Biological speciesTHERMOANAEROBACTER TENGCONGENSIS (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsZhang, Q. / Law, R.H.P. / Bottomley, S.P. / Whisstock, J.C. / Buckle, A.M.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: A Structural Basis for Loop C-Sheet Polymerization in Serpins.
Authors: Zhang, Q. / Law, R.H. / Bottomley, S.P. / Whisstock, J.C. / Buckle, A.M.
History
DepositionNov 19, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 8, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Jul 12, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TENGPIN
B: TENGPIN


Theoretical massNumber of molelcules
Total (without water)86,2242
Polymers86,2242
Non-polymers00
Water4,324240
1
A: TENGPIN


Theoretical massNumber of molelcules
Total (without water)43,1121
Polymers43,1121
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: TENGPIN


Theoretical massNumber of molelcules
Total (without water)43,1121
Polymers43,1121
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)42.895, 68.669, 137.651
Angle α, β, γ (deg.)90.00, 93.45, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Ens-ID: 1 / Refine code: 6

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALAALATHRTHRAA96 - 10354 - 61
21ALAALATHRTHRBB96 - 10354 - 61
12ALAALAASPASPAA168 - 176126 - 134
22ALAALAASPASPBB168 - 176126 - 134
13PHEPHETHRTHRAA316 - 327274 - 285
23PHEPHETHRTHRBB316 - 327274 - 285
14SERSERPROPROAA330 - 339288 - 297
24SERSERPROPROBB330 - 339288 - 297

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Components

#1: Protein TENGPIN / SERINE PROTEASE INHIBITOR


Mass: 43111.977 Da / Num. of mol.: 2 / Fragment: SERPIN, RESIDUES 43-423
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) THERMOANAEROBACTER TENGCONGENSIS (bacteria)
Strain: MB4 / Plasmid: PET-3A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ROSSETTABLUE(DE3)PLYSS / References: UniProt: Q8R9P5
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 240 / 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: 1.8 Å3/Da / Density % sol: 47.3 % / Description: NONE
Crystal growpH: 5.8
Details: 100MM BIS-TRIS, PH5.8, 14% (W/V) PEG 5000, MONOMETHYL ETHER

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418
DetectorType: RIGAKU-MSC / Detector: IMAGE PLATE / Date: Sep 24, 2004 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.45→137.3 Å / Num. obs: 28981 / % possible obs: 98.3 % / Observed criterion σ(I): 2.2 / Redundancy: 3.4 % / Rmerge(I) obs: 0.01 / Net I/σ(I): 14.4
Reflection shellHighest resolution: 2.45 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.05 / Mean I/σ(I) obs: 2.2 / % possible all: 91.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2PEF

2pef


Resolution: 2.45→137.36 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.874 / SU B: 18.515 / SU ML: 0.213 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.671 / ESU R Free: 0.309 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.262 1474 5.1 %RANDOM
Rwork0.192 ---
obs0.196 27494 98.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.15 Å2
Baniso -1Baniso -2Baniso -3
1-0.1 Å20 Å2-0.16 Å2
2--0.02 Å20 Å2
3----0.14 Å2
Refinement stepCycle: LAST / Resolution: 2.45→137.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5845 0 0 240 6085
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0225960
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.9891.968088
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4225751
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.95826.22254
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.786151020
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.39154
X-RAY DIFFRACTIONr_chiral_restr0.0690.2939
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.024432
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1770.22611
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2990.24158
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1170.2315
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1820.272
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1320.215
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.84433865
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.51856072
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.42472382
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.547102016
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 281 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
loose positional0.225
loose thermal3.8810
LS refinement shellResolution: 2.45→2.52 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.349 101
Rwork0.271 1818
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)
10.4501-0.19120.0670.3675-0.0530.29850.00510.00530.01560.00820.00710.01390.03740.0383-0.0122-0.0184-0.00410.0111-0.02910.0036-0.01165.330367.468114.5969
20.22390.1989-0.00030.4827-0.35660.8752-0.03920.01140.0035-0.09060.10930.01990.1022-0.0835-0.0701-0.0067-0.02030.00190.00440.0154-0.03431.709546.269451.6774
30.29350.334-0.08020.816-0.36490.5223-0.0081-0.03710.0203-0.04650.05430.02060.0730.022-0.04620.0111-0.0020.00980.0239-0.0066-0.043437.376345.620958.1281
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 380
2X-RAY DIFFRACTION2B1 - 237
3X-RAY DIFFRACTION3B245 - 381

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