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- PDB-1xpj: Crystal Structure of MCSG Target APC26283 from Vibrio cholerae -

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Basic information

Entry
Database: PDB / ID: 1xpj
TitleCrystal Structure of MCSG Target APC26283 from Vibrio cholerae
Componentshypothetical protein
Keywordsstructural genomics / unknown function / Hypothetical Protein / MCSG / protein structure initiative / PSI / Midwest Center for Structural Genomics
Function / homology
Function and homology information


Capsule biosynthesis phosphatase / haloacid dehalogenase-like hydrolase / HAD superfamily/HAD-like / HAD superfamily / HAD-like superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / L(+)-TARTARIC ACID / Uncharacterized protein
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.3 Å
AuthorsBrunzelle, J.S. / Minasov, G. / Shuvalova, L. / Collart, F.R. / Anderson, W.F. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal Structure of MCSG Target APC26283 from Vibrio cholerae
Authors: Brunzelle, J.S. / Minasov, G. / Shuvalova, L. / Collart, F.R. / Anderson, W.F. / Midwest Center for Structural Genomics (MCSG)
History
DepositionOct 8, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 19, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Sep 26, 2012Group: Database references
Revision 1.4Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.5Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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_alt_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_alt_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.pdbx_ptnr1_label_alt_id / _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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)60,06912
Polymers58,6674
Non-polymers1,4038
Water4,378243
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11700 Å2
ΔGint-151 kcal/mol
Surface area22420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.729, 52.888, 72.215
Angle α, β, γ (deg.)90.00, 90.20, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
hypothetical protein /


Mass: 14666.641 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Plasmid: pMCSG7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21-DE3 / References: UniProt: Q9KVB4
#2: Chemical
ChemComp-HG / MERCURY (II) ION / Mercury (element)


Mass: 200.590 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Hg
#3: Chemical
ChemComp-TLA / L(+)-TARTARIC ACID / Tartaric acid


Mass: 150.087 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H6O6
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 243 / 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: 2.7 Å3/Da / Density % sol: 51.39 %
Crystal growTemperature: 295 K / pH: 6.6
Details: 0.2M di-Ammonium Tartrate, 20% w/v PEG 3350, HgCl2, 5% PEG 4000, pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K, pH 6.60

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Data collection

DiffractionMean temperature: 99.8 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 5ID-B / Wavelength: 0.97818
DetectorType: MARRESEARCH / Detector: CCD / Date: Aug 5, 2004 / Details: MIRROR
RadiationMonochromator: DIAMOND 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97818 Å / Relative weight: 1
ReflectionResolution: 2.15→25 Å / Num. obs: 30494 / % possible obs: 1 % / Observed criterion σ(I): -3 / Redundancy: 7.44 % / Biso Wilson estimate: 41.5 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 18.68
Reflection shellResolution: 2.15→2.27 Å / Redundancy: 5.73 % / Rmerge(I) obs: 0.317 / Mean I/σ(I) obs: 4.98 / % possible all: 0.9

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MAR345data collection
XDSdata scaling
SHELXDphasing
SHARPphasing
RefinementMethod to determine structure: SIRAS / Resolution: 2.3→25 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.92 / SU B: 7.918 / SU ML: 0.188 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.417 / ESU R Free: 0.259 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.253 1315 5 %RANDOM
Rwork0.201 ---
obs0.203 24796 99.1 %-
all-26111 --
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: 24.65 Å2
Baniso -1Baniso -2Baniso -3
1--2.1 Å20 Å2-0.08 Å2
2--4.05 Å20 Å2
3----1.94 Å2
Refinement stepCycle: LAST / Resolution: 2.3→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4054 0 44 243 4341
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0224551
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1911.9646125
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7875490
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0870.2647
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023406
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1960.22185
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1530.2272
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.180.224
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1030.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.3961.52459
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.75124103
X-RAY DIFFRACTIONr_scbond_it1.18832092
X-RAY DIFFRACTIONr_scangle_it1.9024.52022
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.316 95
Rwork0.256 1787
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)
12.68850.0646-0.65192.5526-1.23396.2973-0.0086-0.2078-0.07080.1801-0.0059-0.159-0.09970.53250.01440.02470.00520.01040.0276-0.00390.102632.7215-0.12343.0522
27.3225-5.99053.2477.1245-2.10526.8294-0.0532-0.6218-0.46960.31840.03170.41340.52780.04720.02150.1010.03460.03960.1774-0.04410.087719.5832-2.803954.9016
33.3192-0.48460.62463.9157-3.246.9805-0.04660.57520.2392-0.2171-0.0786-0.29670.05110.44480.12520.04850.01240.00260.13140.00570.09532.79830.329417.9826
48.51395.2441-2.39865.402-1.06945.7356-0.09131.0410.4391-0.40780.06170.3167-0.5361-0.22780.02960.20470.0239-0.03030.4002-0.00880.082819.99592.56856.1817
53.5023-0.417-0.50373.35682.76237.374-0.09360.5383-0.2328-0.2367-0.01250.28210.0657-0.38510.1060.0447-0.0087-0.00050.1016-0.0070.09815.9764-0.560617.98
68.45686.00843.45315.89142.77035.4323-0.0121.1223-0.5826-0.3702-0.0414-0.42650.39630.15390.05350.24480.0310.04320.39180.02820.119619.1544-2.90216.1154
72.99310.12910.42043.16881.46546.70720.0175-0.24160.08950.1012-0.01030.20750.0846-0.4571-0.00730.0058-0.0089-0.02050.04890.0030.09555.8773-0.104943.0466
86.8275-5.4768-3.37267.51242.01357.0386-0.0107-0.70360.38930.4773-0.0771-0.4337-0.3973-0.00410.08780.09610.0283-0.06050.17210.03690.074618.70092.504254.7538
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 871 - 87
2X-RAY DIFFRACTION2AA88 - 12488 - 124
3X-RAY DIFFRACTION3BB1 - 871 - 87
4X-RAY DIFFRACTION4BB88 - 12388 - 123
5X-RAY DIFFRACTION5CC1 - 871 - 87
6X-RAY DIFFRACTION6CC88 - 12388 - 123
7X-RAY DIFFRACTION7DD1 - 871 - 87
8X-RAY DIFFRACTION8DD88 - 12388 - 123

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