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- PDB-4hv4: 2.25 Angstrom resolution crystal structure of UDP-N-acetylmuramat... -

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Basic information

Entry
Database: PDB / ID: 4hv4
Title2.25 Angstrom resolution crystal structure of UDP-N-acetylmuramate--L-alanine ligase (murC) from Yersinia pestis CO92 in complex with AMP
ComponentsUDP-N-acetylmuramate--L-alanine ligase
KeywordsLIGASE / UDP-N-acetylmuramate-L-alanine ligase / murC / Yersinia pestis CO92 / peptidoglycan synthesis / Center for Structural Genomics of Infectious Diseases (CSGID) / NIAID / National Institute of Allergy and Infectious Diseases
Function / homology
Function and homology information


UDP-N-acetylmuramate-L-alanine ligase / UDP-N-acetylmuramate-L-alanine ligase activity / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / cell division / ATP binding / cytoplasm
Similarity search - Function
UDP-N-acetylmuramate--L-alanine ligase / : / Mur ligase, N-terminal catalytic domain / Mur ligase family, catalytic domain / Mur ligase, C-terminal domain / Mur-like, catalytic domain / Mur ligase, C-terminal / Mur ligase, C-terminal domain superfamily / Mur ligase, glutamate ligase domain / Mur ligase, central ...UDP-N-acetylmuramate--L-alanine ligase / : / Mur ligase, N-terminal catalytic domain / Mur ligase family, catalytic domain / Mur ligase, C-terminal domain / Mur-like, catalytic domain / Mur ligase, C-terminal / Mur ligase, C-terminal domain superfamily / Mur ligase, glutamate ligase domain / Mur ligase, central / Mur-like, catalytic domain superfamily / Mur ligase middle domain / UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase / Protein-Tyrosine Phosphatase; Chain A / NAD(P)-binding Rossmann-like Domain / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / BETA-MERCAPTOETHANOL / UDP-N-acetylmuramate--L-alanine ligase
Similarity search - Component
Biological speciesYersinia pestis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsHalavaty, A.S. / Minasov, G. / Dubrovska, I. / Winsor, J. / Shuvalova, L. / Peterson, S. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: 2.25 Angstrom resolution crystal structure of UDP-N-acetylmuramate--L-alanine ligase (murC) from Yersinia pestis CO92 in complex with AMP
Authors: Halavaty, A.S. / Minasov, G. / Dubrovska, I. / Winsor, J. / Shuvalova, L. / Peterson, S. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionNov 5, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 21, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _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: UDP-N-acetylmuramate--L-alanine ligase
B: UDP-N-acetylmuramate--L-alanine ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,8376
Polymers107,9862
Non-polymers8514
Water5,080282
1
A: UDP-N-acetylmuramate--L-alanine ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,4183
Polymers53,9931
Non-polymers4252
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: UDP-N-acetylmuramate--L-alanine ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,4183
Polymers53,9931
Non-polymers4252
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)66.534, 78.021, 183.296
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein UDP-N-acetylmuramate--L-alanine ligase / UDP-N-acetylmuramoyl-L-alanine synthetase


Mass: 53993.043 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pestis (bacteria) / Strain: CO92 / Gene: murC, y3625, YPO0556, YP_3628 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Magic
References: UniProt: Q8ZIE8, UDP-N-acetylmuramate-L-alanine ligase
#2: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#3: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 282 / 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: 2.2 Å3/Da / Density % sol: 44.16 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Protein 7.4 mg/mL in 10 mM Tris-HCl pH8.3 0.5 M NaCl 5 mM BME, 1 mM ADP, 1 mM MgCl2 Crystallization: The PACT Suite (G7) - 0.2 M Sodium acetate 0.1 M Bis Tris propane pH 7.5 20% (w/v) PEG ...Details: Protein 7.4 mg/mL in 10 mM Tris-HCl pH8.3 0.5 M NaCl 5 mM BME, 1 mM ADP, 1 mM MgCl2 Crystallization: The PACT Suite (G7) - 0.2 M Sodium acetate 0.1 M Bis Tris propane pH 7.5 20% (w/v) PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 25, 2012 / Details: Be Lenses
RadiationMonochromator: Diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.25→30 Å / Num. all: 45997 / Num. obs: 45997 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 6.9 % / Biso Wilson estimate: 36.8 Å2 / Rmerge(I) obs: 0.093 / Net I/σ(I): 17.8
Reflection shellResolution: 2.25→2.29 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.554 / Mean I/σ(I) obs: 3.68 / Num. unique all: 2259 / % possible all: 98.2

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Processing

Software
NameVersionClassification
Blu-IceMaxdata collection
PHASERphasing
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2F00

2f00


Resolution: 2.25→29.7 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.938 / SU B: 13.24 / SU ML: 0.15 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R: 0.314 / ESU R Free: 0.215 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22437 2317 5.1 %RANDOM
Rwork0.1795 ---
obs0.18184 43511 99.28 %-
all-43511 --
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: 31.203 Å2
Baniso -1Baniso -2Baniso -3
1--1.41 Å20 Å20 Å2
2---1.1 Å2-0 Å2
3---2.5 Å2
Refinement stepCycle: LAST / Resolution: 2.25→29.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7099 0 54 282 7435
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0217474
X-RAY DIFFRACTIONr_bond_other_d0.0010.025011
X-RAY DIFFRACTIONr_angle_refined_deg1.5891.96210175
X-RAY DIFFRACTIONr_angle_other_deg0.867312161
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.5035955
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.79523.277354
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.753151190
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.6771569
X-RAY DIFFRACTIONr_chiral_restr0.0940.21135
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0218538
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021551
X-RAY DIFFRACTIONr_mcbond_it0.9151.54696
X-RAY DIFFRACTIONr_mcbond_other0.2481.51915
X-RAY DIFFRACTIONr_mcangle_it1.69127554
X-RAY DIFFRACTIONr_scbond_it2.88132778
X-RAY DIFFRACTIONr_scangle_it4.484.52621
LS refinement shellResolution: 2.25→2.308 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.273 179 -
Rwork0.206 3150 -
obs-3150 98.32 %
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)
13.1314-0.1355-0.02444.11211.31491.88390.012-0.20310.3010.13630.01690.2266-0.1742-0.1245-0.02880.07760.01930.00930.1793-0.02570.12059.829936.492633.3843
21.23720.02420.16071.0499-0.19081.5917-0.00260.0173-0.0646-0.2089-0.0527-0.01280.03580.04860.05520.06090.0361-0.01330.0376-0.01950.018529.09627.96213.0233
31.22550.26430.92021.24970.45521.50960.00090.01010.0664-0.0302-0.0148-0.018-0.0285-0.03790.01390.14620.0128-0.04430.0756-0.00570.020511.703946.96820.5694
44.1006-0.5716-0.94532.52820.88743.45710.0062-0.1423-0.1378-0.0073-0.03150.16040.0666-0.05460.02530.0228-0.02910.01280.04940.00170.07313.109659.24660.0237
50.71210.17860.12570.8769-0.06751.82320.0096-0.01060.0238-0.0345-0.066-0.03710.01040.12050.05640.01090.01470.00440.02730.00860.004731.408268.923438.9709
61.6341-0.95670.00861.7634-0.02511.2626-0.0529-0.0318-0.152-0.06260.03310.3393-0.0386-0.32140.01970.04650.0006-0.02020.11070.00010.06748.628773.104127.2686
72.82616.364-8.898733.0681-24.027728.87110.0461-0.00020.1218-0.4590.54441.2375-0.0083-0.1346-0.59050.2755-0.044-0.13760.3104-0.02960.141123.054336.36996.5723
84.2617.9522-2.300714.8419-4.29361.2424-0.19210.0979-0.0398-0.35270.1843-0.08130.0988-0.0510.00790.18160.01240.04020.1826-0.04870.279920.771372.503432.8934
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A19 - 108
2X-RAY DIFFRACTION2A109 - 325
3X-RAY DIFFRACTION3A326 - 483
4X-RAY DIFFRACTION4B15 - 107
5X-RAY DIFFRACTION5B108 - 305
6X-RAY DIFFRACTION6B306 - 483
7X-RAY DIFFRACTION7A501
8X-RAY DIFFRACTION8B501

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