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Basic information

Entry
Database: PDB / ID: 1vj2
TitleCrystal structure of a novel family of manganese-containing cupin (tm1459) from thermotoga maritima at 1.65 A resolution
Componentsnovel manganese-containing cupin TM1459
KeywordsMETAL BINDING PROTEIN / Novel manganese-containing cupin / structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI
Function / homology
Function and homology information


Cupin 2, conserved barrel / Cupin domain / RmlC-like cupin domain superfamily / Jelly Rolls / RmlC-like jelly roll fold / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
: / Unknown ligand / Cupin type-2 domain-containing protein
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: Proteins / Year: 2004
Title: Crystal structure of a novel manganese-containing cupin (TM1459) from Thermotoga maritima at 1.65 A resolution.
Authors: Jaroszewski, L. / Schwarzenbacher, R. / von Delft, F. / McMullan, D. / Brinen, L.S. / Canaves, J.M. / Dai, X. / Deacon, A.M. / DiDonato, M. / Elsliger, M.A. / Eshagi, S. / Floyd, R. / ...Authors: Jaroszewski, L. / Schwarzenbacher, R. / von Delft, F. / McMullan, D. / Brinen, L.S. / Canaves, J.M. / Dai, X. / Deacon, A.M. / DiDonato, M. / Elsliger, M.A. / Eshagi, S. / Floyd, R. / Godzik, A. / Grittini, C. / Grzechnik, S.K. / Hampton, E. / Levin, I. / Karlak, C. / Klock, H.E. / Koesema, E. / Kovarik, J.S. / Kreusch, A. / Kuhn, P. / Lesley, S.A. / McPhillips, T.M. / Miller, M.D. / Morse, A. / Moy, K. / Ouyang, J. / Page, R. / Quijano, K. / Reyes, R. / Rezezadeh, F. / Robb, A. / Sims, E. / Spraggon, G. / Stevens, R.C. / van den Bedem, H. / Velasquez, J. / Vincent, J. / Wang, X. / West, B. / Wolf, G. / Xu, Q. / Hodgson, K.O. / Wooley, J. / Wilson, I.A.
History
DepositionDec 3, 2003Deposition site: RCSB / Processing site: RCSB
SupersessionDec 9, 2003ID: 1O5N
Revision 1.0Dec 9, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Jul 18, 2018Group: Data collection / Database references / Category: pdbx_database_related
Revision 1.5Jan 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.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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Remark 600HETEROGEN THE ACTIVE SITE OF SUBUNIT A NEAR CYS106 HAS BEEN MODELED AS TYPE UNL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: novel manganese-containing cupin TM1459
B: novel manganese-containing cupin TM1459
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2915
Polymers29,1812
Non-polymers1103
Water3,045169
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3990 Å2
ΔGint-44 kcal/mol
Surface area10240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.550, 52.550, 96.267
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

#1: Protein novel manganese-containing cupin TM1459


Mass: 14590.701 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: TM1459 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9X1H0
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 1 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 169 / 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: 2.71 Å3/Da / Density % sol: 54.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 5.2
Details: 50% (v/v) PEG-200, 0.1M Phosphate-citrate pH 4.2 0.2M NaCl, pH 5.2, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 293K
Crystal grow
*PLUS
pH: 7.9 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
120 mMTris1droppH7.9
2150 mM1dropNaCl
30.25 mMTCEP1drop
410 mg/mlprotein1drop
550 %PEG2001reservoir
60.2 M1reservoirNaCl
70.1 Msodium phosphate-citrate1reservoirpH4.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.972386
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 9, 2002 / Details: flat mirror
RadiationMonochromator: single crystal Si(311) bent monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.972386 Å / Relative weight: 1
ReflectionResolution: 1.65→48.13 Å / Num. all: 35029 / Num. obs: 35029 / % possible obs: 97.8 % / Redundancy: 3.6 % / Biso Wilson estimate: 30.49 Å2 / Rsym value: 0.057 / Net I/σ(I): 15.6
Reflection shellResolution: 1.65→1.74 Å / Redundancy: 2.7 % / Mean I/σ(I) obs: 1.9 / Num. unique all: 4592 / Rsym value: 0.466 / % possible all: 87.6
Reflection
*PLUS
Highest resolution: 1.65 Å / Num. measured all: 124395 / Rmerge(I) obs: 0.067
Reflection shell
*PLUS
% possible obs: 87.6 % / Rmerge(I) obs: 0.577

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALA4.2)data scaling
MOLREPphasing
REFMACrefinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FI2

1fi2


Resolution: 1.65→33.07 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.937 / SU B: 6.097 / SU ML: 0.097 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / ESU R: 0.1 / ESU R Free: 0.104 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. THE BOUND METAL WAS IDENTIFIED AS TRANSITION METAL BY ITS COORDINATION GEOMETRY, AND AS MANGANESE BY COMPARISON WITH THE HOMOLOGOUS ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. THE BOUND METAL WAS IDENTIFIED AS TRANSITION METAL BY ITS COORDINATION GEOMETRY, AND AS MANGANESE BY COMPARISON WITH THE HOMOLOGOUS STRUCTURE TM1287 (1O4T) AS WELL AS BY HAVING BEST B-FACTOR AGREEMENT WITH SURROUNDING ATOMS. 3. THE ACTIVE SITE OF SUBUNIT A NEAR CYS106 HAS BEEN MODELED AS TYPE UNL.
RfactorNum. reflection% reflectionSelection details
Rfree0.24859 1729 4.9 %RANDOM
Rwork0.20817 ---
obs0.21015 33262 97.78 %-
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: 24.615 Å2
Baniso -1Baniso -2Baniso -3
1-0.98 Å20.49 Å20 Å2
2--0.98 Å20 Å2
3----1.47 Å2
Refinement stepCycle: LAST / Resolution: 1.65→33.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1850 0 6 169 2025
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0221890
X-RAY DIFFRACTIONr_bond_other_d0.0010.021754
X-RAY DIFFRACTIONr_angle_refined_deg1.6521.9582548
X-RAY DIFFRACTIONr_angle_other_deg0.85434090
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9715226
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.82923.91392
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.15715350
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.5961514
X-RAY DIFFRACTIONr_chiral_restr0.1030.2278
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022070
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02382
X-RAY DIFFRACTIONr_nbd_refined0.1860.2326
X-RAY DIFFRACTIONr_nbd_other0.1930.21738
X-RAY DIFFRACTIONr_nbtor_other0.0910.21274
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0540.22
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1370.29
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2720.226
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1510.210
X-RAY DIFFRACTIONr_mcbond_it1.1791.51472
X-RAY DIFFRACTIONr_mcangle_it1.35121844
X-RAY DIFFRACTIONr_scbond_it2.5093860
X-RAY DIFFRACTIONr_scangle_it3.3384.5704
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.386 100 4.43 %
Rwork0.31 2159 -
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)
11.08660.2610.16282.58190.12443.085-0.1230.13560.0144-0.23570.1545-0.2043-0.01590.1418-0.0314-0.0697-0.07590.0396-0.1221-0.0145-0.071430.94882.1018-1.118
20.7375-0.208-0.31282.6298-0.0483.1667-0.1185-0.0741-0.05780.22930.1742-0.22280.1390.2142-0.0557-0.05130.0795-0.0339-0.1289-0.0264-0.050832.7388-0.6720.0896
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA6 - 11418 - 126
21BB1 - 513 - 17
32BB6 - 11418 - 126
42AA1 - 513 - 17
Software
*PLUS
Name: REFMAC / Version: 5.1.9999 / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.249 / Rfactor Rwork: 0.208
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.018
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg1.65
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scangle_it

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