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- PDB-1ztc: Crystal structure of a putative metallo-beta-lactamase (tm0894) f... -

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Basic information

Entry
Database: PDB / ID: 1ztc
TitleCrystal structure of a putative metallo-beta-lactamase (tm0894) from Thermotoga maritima at 2.10 A resolution
Componentshypothetical protein TM0894
KeywordsHYDROLASE / Structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI
Function / homology
Function and homology information


Metallo-beta-lactamase domain-containing protein 1 / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase superfamily / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase; Chain A / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
NICKEL (II) ION / PHOSPHATE ION / Metallo-beta-lactamase domain-containing protein 1
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of hypothetical protein (tm0894) from Thermotoga maritima at 2.10 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionMay 26, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 28, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Jan 25, 2023Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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.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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 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
Remark 300BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 4 CHAIN(S) ...BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 4 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). SIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF A TETRAMER AS THE BIOLOGICALLY RELEVANT OLIGIMERIZATION STATE.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: hypothetical protein TM0894
B: hypothetical protein TM0894
C: hypothetical protein TM0894
D: hypothetical protein TM0894
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,86222
Polymers102,3274
Non-polymers1,53518
Water8,179454
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14240 Å2
ΔGint-220 kcal/mol
Surface area29960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.783, 127.343, 152.224
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: HIS / Beg label comp-ID: HIS / Refine code: 2

Dom-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1GLUGLUAA-1 - 20611 - 218
2GLUGLUBB-1 - 20611 - 218
3PROPROCC-1 - 20511 - 217
4GLUGLUDD-1 - 20611 - 218

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Components

#1: Protein
hypothetical protein TM0894


Mass: 25581.805 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: tm0894 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9WZZ6
#2: Chemical
ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ni
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: PO4
#4: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 454 / 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: 4.23 Å3/Da / Density % sol: 70.67 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 6.3
Details: 35.0% MPD, 0.1M Na,K-Phosphate, pH 6.3, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.946415, 0.979413
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 3, 2005
Details: Flat mirror (vertical focusing), single crystal Si(111) bent monochromator (horizontal focusing)
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9464151
20.9794131
ReflectionResolution: 2.1→29.93 Å / Num. obs: 100112 / % possible obs: 98 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.048 / Rsym value: 0.048 / Net I/σ(I): 10.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)% possible obs (%)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsRsym value
2.1-2.2188.62.70.4131.9129390.413
2.21-2.3599.53.40.2712.8139220.271
2.35-2.5199.93.60.1794.3131560.179
2.51-2.711003.60.1216.3123070.121
2.71-2.9799.93.60.0749.9113100.074
2.97-3.3299.83.60.0513.4102800.05
3.32-3.8399.83.50.03219.790810.032
3.83-4.799.63.50.0321777370.032
4.7-6.6498.43.20.03514.459540.035
6.64-29.93983.40.02222.534260.022

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0005refinement
SCALAdata scaling
MOSFLMdata reduction
CCP4(SCALA)data scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.1→29.6 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.962 / SU B: 5.928 / SU ML: 0.078 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.113 / ESU R Free: 0.107
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. X-RAY FLUORESCENCE SUPPORTS THE ASSIGNMENT OF THE METAL SITES AS NICKEL. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. X-RAY FLUORESCENCE SUPPORTS THE ASSIGNMENT OF THE METAL SITES AS NICKEL. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.7 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION.
RfactorNum. reflection% reflectionSelection details
Rfree0.178 5004 5 %RANDOM
Rwork0.157 ---
all0.159 ---
obs0.15855 95035 97.81 %-
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: 44.232 Å2
Baniso -1Baniso -2Baniso -3
1-0.67 Å20 Å20 Å2
2---1.91 Å20 Å2
3---1.24 Å2
Refinement stepCycle: LAST / Resolution: 2.1→29.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6769 0 73 454 7296
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0227057
X-RAY DIFFRACTIONr_bond_other_d0.0020.026472
X-RAY DIFFRACTIONr_angle_refined_deg1.3661.9569583
X-RAY DIFFRACTIONr_angle_other_deg0.812315016
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5815829
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.32423.512336
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.598151211
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3051539
X-RAY DIFFRACTIONr_chiral_restr0.0820.21085
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.027646
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021477
X-RAY DIFFRACTIONr_nbd_refined0.1970.21348
X-RAY DIFFRACTIONr_nbd_other0.1820.26765
X-RAY DIFFRACTIONr_nbtor_refined0.1790.23386
X-RAY DIFFRACTIONr_nbtor_other0.0840.24237
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1360.2451
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.180.26
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3180.231
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1140.26
X-RAY DIFFRACTIONr_mcbond_it1.93134916
X-RAY DIFFRACTIONr_mcbond_other0.42531694
X-RAY DIFFRACTIONr_mcangle_it2.58656797
X-RAY DIFFRACTIONr_scbond_it4.69183251
X-RAY DIFFRACTIONr_scangle_it6.363112786
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1220tight positional0.050.05
2B1220tight positional0.040.05
3C1220tight positional0.040.05
4D1220tight positional0.040.05
1A1911medium positional0.420.5
2B1911medium positional0.320.5
3C1911medium positional0.350.5
4D1911medium positional0.320.5
1A1220tight thermal0.180.5
2B1220tight thermal0.140.5
3C1220tight thermal0.140.5
4D1220tight thermal0.160.5
1A1911medium thermal0.942
2B1911medium thermal0.762
3C1911medium thermal0.742
4D1911medium thermal0.772
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.275 283 -
Rwork0.233 5940 -
obs--83.33 %
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)
11.9226-0.4606-0.33042.33780.9211.5398-0.0530.3108-0.0005-0.19650.0255-0.0758-0.1404-0.05210.0275-0.2604-0.0168-0.0302-0.134-0.0188-0.288235.44595.6040.225
21.70640.40170.75743.06770.98811.55150.0073-0.08210.0430.19370.0594-0.2988-0.02260.0515-0.0666-0.18830.018-0.1237-0.2014-0.0582-0.178249.715110.16733.474
32.1477-0.15820.77832.32110.9372.057-0.1016-0.22420.36910.0586-0.12470.2115-0.2202-0.26880.2263-0.21890.076-0.0721-0.148-0.081-0.147618.662114.57224.048
41.21380.1360.1472.6908-0.19561.57780.0298-0.0573-0.1640.18850.0358-0.06680.0304-0.0668-0.0656-0.21120.0262-0.0678-0.21690.0329-0.199734.72379.21728.492
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-1 - 207
2X-RAY DIFFRACTION2B-1 - 207
3X-RAY DIFFRACTION3C-1 - 205
4X-RAY DIFFRACTION4D-1 - 206

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