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- PDB-2wkn: gamma lactamase from Delftia acidovorans -

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Basic information

Entry
Database: PDB / ID: 2wkn
Titlegamma lactamase from Delftia acidovorans
ComponentsFORMAMIDASE
KeywordsHYDROLASE / BIOCATALYSIS
Function / homologyAcetamidase/Formamidase / Acetamidase/Formamidase family / formamidase / formamidase activity / metal ion binding / Formamidase
Function and homology information
Biological speciesDELFTIA ACIDOVORANS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.08 Å
AuthorsIsupov, M.N. / Line, K. / Gonsalvez, I.S. / Gange-Harris, P. / Lanzotti, M. / Saneei, V. / Littlechild, J.A.
Citation
Journal: To be Published
Title: The Structure of Gamma Lactamase from Delftia Acidovorans
Authors: Isupov, M.N. / Line, K. / Gonsalvez, I.S. / Gange-Harris, P. / Lanzotti, M. / Saneei, V. / Littlechild, J.A.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2001
Title: Crystallization and Preliminary X-Ray Analysis of a Gamma-Lactamase.
Authors: Gonsalvez, I.S. / Isupov, M.N. / Littlechild, J.A.
History
DepositionJun 16, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 1, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / struct_site
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 / _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.pdbx_dist_value / _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 / _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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_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: FORMAMIDASE
B: FORMAMIDASE
C: FORMAMIDASE
D: FORMAMIDASE
E: FORMAMIDASE
F: FORMAMIDASE
G: FORMAMIDASE
H: FORMAMIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)356,78324
Polymers355,7378
Non-polymers1,04716
Water33,2921848
1
A: FORMAMIDASE
B: FORMAMIDASE
C: FORMAMIDASE
D: FORMAMIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)178,39212
Polymers177,8684
Non-polymers5238
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19770 Å2
ΔGint-420.5 kcal/mol
Surface area49090 Å2
MethodPISA
2
E: FORMAMIDASE
F: FORMAMIDASE
G: FORMAMIDASE
H: FORMAMIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)178,39212
Polymers177,8684
Non-polymers5238
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19780 Å2
ΔGint-420.1 kcal/mol
Surface area49220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.871, 94.621, 152.297
Angle α, β, γ (deg.)105.71, 90.27, 108.46
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71G
81H
12A
22C
32D
42E
52F
62G
72H

NCS domain segments:

Refine code: 1

Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111THRTHRALAALAAA4 - 584 - 58
211THRTHRALAALABB4 - 584 - 58
311THRTHRALAALACC4 - 584 - 58
411THRTHRALAALADD4 - 584 - 58
511THRTHRALAALAEE4 - 584 - 58
611THRTHRALAALAFF4 - 584 - 58
711THRTHRALAALAGG4 - 584 - 58
811THRTHRALAALAHH4 - 584 - 58
121ASPASPPROPROAA63 - 16163 - 161
221ASPASPPROPROBB63 - 16163 - 161
321ASPASPPROPROCC63 - 16163 - 161
421ASPASPPROPRODD63 - 16163 - 161
521ASPASPPROPROEE63 - 16163 - 161
621ASPASPPROPROFF63 - 16163 - 161
721ASPASPPROPROGG63 - 16163 - 161
821ASPASPPROPROHH63 - 16163 - 161
131METMETASNASNAA163 - 168163 - 168
231METMETASNASNBB163 - 168163 - 168
331METMETASNASNCC163 - 168163 - 168
431METMETASNASNDD163 - 168163 - 168
531METMETASNASNEE163 - 168163 - 168
631METMETASNASNFF163 - 168163 - 168
731METMETASNASNGG163 - 168163 - 168
831METMETASNASNHH163 - 168163 - 168
141ARGARGASPASPAA170 - 178170 - 178
241ARGARGASPASPBB170 - 178170 - 178
341ARGARGASPASPCC170 - 178170 - 178
441ARGARGASPASPDD170 - 178170 - 178
541ARGARGASPASPEE170 - 178170 - 178
641ARGARGASPASPFF170 - 178170 - 178
741ARGARGASPASPGG170 - 178170 - 178
841ARGARGASPASPHH170 - 178170 - 178
151ILEILEGLYGLYAA182 - 197182 - 197
251ILEILEGLYGLYBB182 - 197182 - 197
351ILEILEGLYGLYCC182 - 197182 - 197
451ILEILEGLYGLYDD182 - 197182 - 197
551ILEILEGLYGLYEE182 - 197182 - 197
651ILEILEGLYGLYFF182 - 197182 - 197
751ILEILEGLYGLYGG182 - 197182 - 197
851ILEILEGLYGLYHH182 - 197182 - 197
161ALAALAGLYGLYAA207 - 317207 - 317
261ALAALAGLYGLYBB207 - 317207 - 317
361ALAALAGLYGLYCC207 - 317207 - 317
461ALAALAGLYGLYDD207 - 317207 - 317
561ALAALAGLYGLYEE207 - 317207 - 317
661ALAALAGLYGLYFF207 - 317207 - 317
761ALAALAGLYGLYGG207 - 317207 - 317
861ALAALAGLYGLYHH207 - 317207 - 317
171GLNGLNTRPTRPAA319 - 376319 - 376
271GLNGLNTRPTRPBB319 - 376319 - 376
371GLNGLNTRPTRPCC319 - 376319 - 376
471GLNGLNTRPTRPDD319 - 376319 - 376
571GLNGLNTRPTRPEE319 - 376319 - 376
671GLNGLNTRPTRPFF319 - 376319 - 376
771GLNGLNTRPTRPGG319 - 376319 - 376
871GLNGLNTRPTRPHH319 - 376319 - 376
181PROPROALAALAAA378 - 390378 - 390
281PROPROALAALABB378 - 390378 - 390
381PROPROALAALACC378 - 390378 - 390
481PROPROALAALADD378 - 390378 - 390
581PROPROALAALAEE378 - 390378 - 390
681PROPROALAALAFF378 - 390378 - 390
781PROPROALAALAGG378 - 390378 - 390
881PROPROALAALAHH378 - 390378 - 390
191ASPASPASPASPAA402 - 408402 - 408
291ASPASPASPASPBB402 - 408402 - 408
391ASPASPASPASPCC402 - 408402 - 408
491ASPASPASPASPDD402 - 408402 - 408
591ASPASPASPASPEE402 - 408402 - 408
691ASPASPASPASPFF402 - 408402 - 408
791ASPASPASPASPGG402 - 408402 - 408
891ASPASPASPASPHH402 - 408402 - 408
112ALAALAGLNGLNAA2 - 1982 - 198
212ALAALAGLNGLNCC2 - 1982 - 198
312ALAALAGLNGLNDD2 - 1982 - 198
412ALAALAGLNGLNEE2 - 1982 - 198
512ALAALAGLNGLNFF2 - 1982 - 198
612ALAALAGLNGLNGG2 - 1982 - 198
712ALAALAGLNGLNHH2 - 1982 - 198

NCS ensembles :
ID
1
2

NCS oper:
IDCodeMatrixVector
1given(-0.97255, -0.22303, 0.06642), (-0.22066, 0.79317, -0.56762), (0.07392, -0.56669, -0.82061)2.31085, 9.94126, 30.54151
2given(0.9736, 0.20777, -0.09458), (0.20789, -0.97811, -0.00862), (-0.0943, -0.01127, -0.99548)-4.141, 47.16549, 18.87299
3given(-0.99952, 0.00881, 0.0298), (0.00994, -0.81797, 0.57518), (0.02944, 0.5752, 0.81748)-2.86226, 37.67396, -11.86448
4given(0.99985, 0.00101, -0.01747), (0.0009, -0.99998, -0.00625), (-0.01748, 0.00623, -0.99983)-0.64903, 22.07489, -59.84282
5given(-0.99982, -0.00022, 0.01879), (-0.01112, 0.81325, -0.5818), (-0.01516, -0.58191, -0.81311)-3.27111, -15.52011, -47.72132
6given(-0.97475, -0.20881, 0.07918), (0.2161, -0.79255, 0.57023), (-0.05632, 0.57294, 0.81766)1.06251, 11.96786, -90.33325
7given(0.97516, 0.20673, -0.07959), (-0.20613, 0.9784, 0.01572), (0.08112, 0.00108, 0.9967)-5.01542, -25.24104, -78.35248

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Components

#1: Protein
FORMAMIDASE / GAMMA-LACTAMASE


Mass: 44467.078 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DELFTIA ACIDOVORANS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: A9BPK4, formamidase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1848 / 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: 2.35 Å3/Da / Density % sol: 47.4 %
Description: A COMBINATION OF THREE-WAVELENGTH ZN MAD AND HG SIRAS WITH MULTICRYSTAL AVERAGING BETWEEN NON-ISOMORPHOUS CRYSTALS WAS USED FOR STRUCTURE DETERMINATION
Crystal growpH: 5.6
Details: 15% PEG 4000 0.1 M SODIUM ACETATE PH 5.6, 50 MM NACL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.1 / Wavelength: 1.488
DetectorType: ADSC CCD / Detector: CCD / Date: Sep 17, 2004
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.488 Å / Relative weight: 1
ReflectionResolution: 2.08→25 Å / Num. obs: 176148 / % possible obs: 91.2 % / Observed criterion σ(I): 0 / Redundancy: 2 % / Biso Wilson estimate: 35.3 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 11.3
Reflection shellResolution: 2.08→2.19 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 2.1 / % possible all: 72.1

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
MLPHAREphasing
DMphasing
REFMAC5.5.0088refinement
RefinementMethod to determine structure: MAD
Starting model: NONE

Resolution: 2.08→24.78 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.922 / SU B: 8.162 / SU ML: 0.208 / Cross valid method: THROUGHOUT / ESU R: 0.307 / ESU R Free: 0.23 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.269 3457 2 %RANDOM
Rwork0.22 ---
obs0.221 172361 90.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 37.93 Å2
Baniso -1Baniso -2Baniso -3
1-3.69 Å20.64 Å2-1.25 Å2
2---0.77 Å2-2.2 Å2
3----3.71 Å2
Refinement stepCycle: LAST / Resolution: 2.08→24.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms24992 0 16 1848 26856
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.02225781
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3191.95335100
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.32153286
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.56524.8231159
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.039153990
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0351596
X-RAY DIFFRACTIONr_chiral_restr0.090.23720
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02120180
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_it1.759416229
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.953626084
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.14789552
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.639109001
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

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A2803tight positional0.030.05
12B2803tight positional0.040.05
13C2803tight positional0.030.05
14D2803tight positional0.030.05
15E2803tight positional0.030.05
16F2803tight positional0.040.05
17G2803tight positional0.040.05
18H2803tight positional0.030.05
21A1503tight positional0.040.05
22C1503tight positional0.030.05
23D1503tight positional0.020.05
24E1503tight positional0.020.05
25F1503tight positional0.020.05
26G1503tight positional0.030.05
27H1503tight positional0.020.05
11A2803tight thermal0.140.5
12B2803tight thermal0.150.5
13C2803tight thermal0.120.5
14D2803tight thermal0.130.5
15E2803tight thermal0.120.5
16F2803tight thermal0.120.5
17G2803tight thermal0.130.5
18H2803tight thermal0.130.5
21A1503tight thermal0.080.5
22C1503tight thermal0.070.5
23D1503tight thermal0.070.5
24E1503tight thermal0.060.5
25F1503tight thermal0.070.5
26G1503tight thermal0.080.5
27H1503tight thermal0.080.5
LS refinement shellResolution: 2.08→2.14 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.367 167 -
Rwork0.369 8020 -
obs--57.37 %

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