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- PDB-1vjn: Crystal structure of a putative zn-dependent hydrolase of the met... -

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Basic information

Entry
Database: PDB / ID: 1vjn
TitleCrystal structure of a putative zn-dependent hydrolase of the metallo-beta-lactamase superfamily (tm0207) from thermotoga maritima at 2.00 A resolution
ComponentsZn-dependent hydrolase of metallo-beta-lactamase superfamily TM0207
KeywordsHYDROLASE / Metallo-hydrolase/oxidoreductase fold / structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI
Function / homologyBeta-lactamase superfamily domain / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase; Chain A / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / 4-Layer Sandwich / Alpha Beta / MBL fold metallo-hydrolase
Function and homology information
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of Zn-dependent hydrolase of metallo-beta-lactamase superfamily (TM0207) from Thermotoga maritima at 2.00 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionMar 11, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 16, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Jan 25, 2023Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.4Nov 20, 2024Group: Data collection / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Zn-dependent hydrolase of metallo-beta-lactamase superfamily TM0207
B: Zn-dependent hydrolase of metallo-beta-lactamase superfamily TM0207


Theoretical massNumber of molelcules
Total (without water)50,0902
Polymers50,0902
Non-polymers00
Water2,774154
1
A: Zn-dependent hydrolase of metallo-beta-lactamase superfamily TM0207


Theoretical massNumber of molelcules
Total (without water)25,0451
Polymers25,0451
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Zn-dependent hydrolase of metallo-beta-lactamase superfamily TM0207


Theoretical massNumber of molelcules
Total (without water)25,0451
Polymers25,0451
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.147, 45.723, 63.491
Angle α, β, γ (deg.)73.66, 89.25, 64.96
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31A
41B
51A
61B
71A
81B
91A
101B
111A
121B
131A
141B

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11HISHISPROPRO5AA0 - 3212 - 44
21HISHISPROPRO5BB0 - 3212 - 44
32ILEILEASPASP6AA33 - 3945 - 51
42ILEILEASPASP6BB33 - 3945 - 51
53VALVALLEULEU5AA40 - 11652 - 128
63VALVALLEULEU5BB40 - 11652 - 128
74THRTHRGLUGLU6AA117 - 123129 - 135
84THRTHRGLUGLU6BB117 - 123129 - 135
95ILEILETYRTYR5AA124 - 162136 - 174
105ILEILETYRTYR5BB124 - 162136 - 174
116LYSLYSLEULEU6AA163 - 171175 - 183
126LYSLYSLEULEU6BB163 - 171175 - 183
137LEULEUVALVAL5AA172 - 207184 - 219
147LEULEUVALVAL5BB172 - 207184 - 219

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Components

#1: Protein Zn-dependent hydrolase of metallo-beta-lactamase superfamily TM0207


Mass: 25045.146 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: TM0207 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9WY50
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 154 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.16 Å3/Da / Density % sol: 49.9 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 5
Details: 20% PEG-6000, 0.1M citric acid pH 5.0, 1M LiCl, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
1,21
Diffraction source
SourceSiteBeamlineIDWavelengthWavelength (Å)
SYNCHROTRONAPS 19-BM10.97944
SYNCHROTRONSSRL BL9-120.979148, 0.898403
Detector
TypeIDDetectorDateDetails
APS-11CCDOct 26, 2002water cooled, sagitally focusing 2nd crystal, Rosenbaum-Rock vertical focusing mirror
ADSC QUANTUM 3152CCDDec 2, 2002
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Rosenbaum-Rock double-crystal monochromatorMADMx-ray1
2single crystal Si(311) bent monochromatorMADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.979441
20.9791481
30.8984031
ReflectionResolution: 2→50 Å / Num. obs: 26349 / % possible obs: 93.6 % / Redundancy: 2.48 % / Biso Wilson estimate: 40.21 Å2 / Rmerge(I) obs: 0.079 / Net I/σ(I): 10.38
Reflection shellResolution: 2→2.07 Å / Redundancy: 2.19 % / Rmerge(I) obs: 0.441 / Mean I/σ(I) obs: 2.03 / Num. unique all: 2099 / % possible all: 73.47

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALEPACKdata scaling
SOLVEphasing
RESOLVEmodel building
REFMAC5.2.0000refinement
RESOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2→38.91 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.947 / SU B: 9.293 / SU ML: 0.129 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.185 / ESU R Free: 0.162
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21993 1319 5 %RANDOM
Rwork0.1784 ---
obs0.18053 25012 93.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 25.677 Å2
Baniso -1Baniso -2Baniso -3
1-0.97 Å20.19 Å20.97 Å2
2---0.92 Å20.75 Å2
3----0.66 Å2
Refinement stepCycle: LAST / Resolution: 2→38.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2966 0 0 154 3120
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0223030
X-RAY DIFFRACTIONr_bond_other_d0.0030.022810
X-RAY DIFFRACTIONr_angle_refined_deg1.4581.9494100
X-RAY DIFFRACTIONr_angle_other_deg0.75436538
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1895375
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.8624.839124
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.21715516
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.889157
X-RAY DIFFRACTIONr_chiral_restr0.0840.2474
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023296
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02573
X-RAY DIFFRACTIONr_nbd_refined0.210.2492
X-RAY DIFFRACTIONr_nbd_other0.1760.22777
X-RAY DIFFRACTIONr_nbtor_other0.0850.21802
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1830.2125
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2670.210
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1960.229
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2830.26
X-RAY DIFFRACTIONr_mcbond_it2.78531935
X-RAY DIFFRACTIONr_mcbond_other0.6643781
X-RAY DIFFRACTIONr_mcangle_it3.82153058
X-RAY DIFFRACTIONr_scbond_it5.90281217
X-RAY DIFFRACTIONr_scangle_it8.672111042
Refine LS restraints NCS

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

NumberTypeRms dev position (Å)Weight position
966medium positional0.190.5
1841loose positional0.75
966medium thermal0.972
1841loose thermal2.6310
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.319 68 4.84 %
Rwork0.256 1337 -
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)
11.4578-0.3027-0.38412.714-0.13522.13960.0766-0.05810.01460.1969-0.0065-0.032-0.10780.0007-0.07010.12210.00530.04280.043-0.00750.047516.66522.7721.017
22.7467-1.8105-3.93484.00083.18028.90380.14910.55460.12-0.515-0.27750.2225-0.2733-0.80310.12840.15580.02130.01330.18220.05320.1146-1.4235.472-6.455
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL / Auth seq-ID: 1 - 207 / Label seq-ID: 13 - 219

IDRefine TLS-IDAuth asym-IDLabel asym-ID
11AA
22BB

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