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- PDB-1rmd: RAG1 DIMERIZATION DOMAIN -

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Basic information

Entry
Database: PDB / ID: 1rmd
TitleRAG1 DIMERIZATION DOMAIN
ComponentsRAG1
KeywordsDNA BINDING PROTEIN / RAG1 / V(D)J RECOMBINATION / ANTIBODY / MAD / RING FINGER / ZINC BINUCLEAR CLUSTER / ZINC FINGER / DNA-BINDING PROTEIN
Function / homology
Function and homology information


DNA recombinase complex / endodeoxyribonuclease complex / regulation of behavioral fear response / pre-B cell allelic exclusion / V(D)J recombination / negative regulation of T cell apoptotic process / negative regulation of thymocyte apoptotic process / positive regulation of T cell differentiation / regulation of T cell differentiation / T cell homeostasis ...DNA recombinase complex / endodeoxyribonuclease complex / regulation of behavioral fear response / pre-B cell allelic exclusion / V(D)J recombination / negative regulation of T cell apoptotic process / negative regulation of thymocyte apoptotic process / positive regulation of T cell differentiation / regulation of T cell differentiation / T cell homeostasis / protein autoubiquitination / B cell differentiation / thymus development / RING-type E3 ubiquitin transferase / visual learning / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / T cell differentiation in thymus / chromatin organization / histone binding / endonuclease activity / DNA recombination / sequence-specific DNA binding / adaptive immune response / Hydrolases; Acting on ester bonds / protein homodimerization activity / zinc ion binding / nucleoplasm / identical protein binding / metal ion binding / nucleus
Similarity search - Function
Recombination-activating protein 1 zinc-finger domain / V(D)J recombination-activating protein 1, Zinc finger / RAG nonamer-binding domain / NBD domain profile. / Zinc finger RAG1-type profile. / V(D)J recombination-activating protein 1 / RAG1 importin-binding / RAG1 importin binding / Recombination-activation protein 1 (RAG1), recombinase / Classic Zinc Finger ...Recombination-activating protein 1 zinc-finger domain / V(D)J recombination-activating protein 1, Zinc finger / RAG nonamer-binding domain / NBD domain profile. / Zinc finger RAG1-type profile. / V(D)J recombination-activating protein 1 / RAG1 importin-binding / RAG1 importin binding / Recombination-activation protein 1 (RAG1), recombinase / Classic Zinc Finger / Zinc finger, C3HC4 RING-type / Zinc finger, C3HC4 type (RING finger) / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / Double Stranded RNA Binding Domain / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Zinc finger C2H2 superfamily / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
V(D)J recombination-activating protein 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å
AuthorsBellon, S.F. / Rodgers, K.K. / Schatz, D.G. / Coleman, J.E. / Steitz, T.A.
CitationJournal: Nat.Struct.Biol. / Year: 1997
Title: Crystal structure of the RAG1 dimerization domain reveals multiple zinc-binding motifs including a novel zinc binuclear cluster.
Authors: Bellon, S.F. / Rodgers, K.K. / Schatz, D.G. / Coleman, J.E. / Steitz, T.A.
History
DepositionJan 10, 1997Processing site: BNL
Revision 1.0Jul 23, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_conn / struct_keywords / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _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_keywords.text / _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

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Assembly

Deposited unit
A: RAG1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,4135
Polymers13,1511
Non-polymers2624
Water93752
1
A: RAG1
hetero molecules

A: RAG1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,82610
Polymers26,3032
Non-polymers5238
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+2/31
Unit cell
Length a, b, c (Å)57.580, 57.580, 98.430
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein RAG1 / / V(D)J RECOMBINATION ACTIVATING PROTEIN 1


Mass: 13151.449 Da / Num. of mol.: 1 / Fragment: ZINC-BINDING DIMERIZATION DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line: BL21 / Cell line (production host): BL21 / Production host: Escherichia coli (E. coli) / References: UniProt: P15919
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 52 / 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: 3.58 Å3/Da / Density % sol: 65 %
Crystal growpH: 7.5
Details: 5-10 % PEG 4K, 100MM HEPES, PH 7.5, 10% ETHYLENE GLYCOL
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15-10 %PEG40001reservoir
2100 mMHEPES1reservoir
310 %ethylene glycerol1reservoir

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1.35
DetectorType: MARRESEARCH / Detector: IMAGE PLATE AREA DETECTOR / Date: Jun 1, 1996 / Details: MIRRORS
RadiationMonochromator: DOUBLE CRYSTAL SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.35 Å / Relative weight: 1
ReflectionResolution: 2.1→20 Å / Num. obs: 36957 / % possible obs: 93.9 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Biso Wilson estimate: 15.4 Å2 / Rmerge(I) obs: 0.072 / Rsym value: 0.072 / Net I/σ(I): 24
Reflection shellResolution: 2.1→2.15 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.61 / Mean I/σ(I) obs: 3.1 / Rsym value: 0.61 / % possible all: 95.6
Reflection shell
*PLUS
% possible obs: 95.6 %

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Processing

Software
NameVersionClassification
BAZFAZmodel building
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
BAZFAZphasing
RefinementMethod to determine structure: MAD / Resolution: 2.1→20 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / σ(F): 4
Details: LOCAL SCALING USING MAXSCALE WAS USED TO CORRECT THE HIGHLY ANISOTROPIC DATA. THE LOW OVERALL COMPLETION OF THE DATA REFLECT THIS ANISOTROPY.
RfactorNum. reflection% reflectionSelection details
Rfree0.257 668 9.6 %RANDOM
Rwork0.209 ---
obs0.209 6970 60.5 %-
Displacement parametersBiso mean: 28.7 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.25 Å0.21 Å
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms911 0 4 52 967
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.1
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.2
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.47
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2.1→2.2 Å / Rfactor Rfree error: 0.042 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.276 43 10.4 %
Rwork0.259 372 -
obs--29.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PAR.WATTOP_116_117.ZN
X-RAY DIFFRACTION3PAR.ZNTOP_118.ZN
X-RAY DIFFRACTION4TOP_119.ZN
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.2
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.47

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