HEADER PROTEIN BINDING 02-AUG-07 2V86 TITLE CRYSTAL STRUCTURE OF RAG2-PHD FINGER IN COMPLEX WITH H3R2ME2AK4ME3 TITLE 2 PEPTIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: VDJ RECOMBINATION-ACTIVATING PROTEIN 2; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: RESIDUES 414-487; COMPND 5 SYNONYM: RAG2, RAG2-PHD FINGER; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: H3R2ME2AK4ME3 PEPTIDE; COMPND 9 CHAIN: D, E; COMPND 10 FRAGMENT: H3 (1-21), BIOTINILATED AT C-TERMINUS; COMPND 11 ENGINEERED: YES; COMPND 12 OTHER_DETAILS: R2 ASYMMETRICALLY DIMETHYLATED AND K4 TRIMETHYLATED SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: HOUSE MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PGEX-6P-1; SOURCE 10 MOL_ID: 2; SOURCE 11 SYNTHETIC: YES; SOURCE 12 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 13 ORGANISM_COMMON: HOUSE MOUSE; SOURCE 14 ORGANISM_TAXID: 10090 KEYWDS V(D)J RECOMBINATION, COVALENT MODIFICATIONS, RAG2, HISTONE, NUCLEUS, KEYWDS 2 NUCLEASE, HYDROLASE, PHD FINGER, DNA-BINDING, RECOMBINASE, KEYWDS 3 ENDONUCLEASE, TRIMETHYL LYSINE, DIMETHYL ARGININE, DNA KEYWDS 4 RECOMBINATION, PROTEIN BINDING EXPDTA X-RAY DIFFRACTION AUTHOR S.RAMON-MAIQUES,W.YANG REVDAT 8 13-DEC-23 2V86 1 REMARK LINK REVDAT 7 08-MAY-19 2V86 1 REMARK REVDAT 6 06-MAR-19 2V86 1 REMARK SEQRES LINK REVDAT 5 08-FEB-17 2V86 1 SOURCE REMARK DBREF SEQADV REVDAT 5 2 1 FORMUL REVDAT 4 06-NOV-13 2V86 1 REMARK HETSYN HETATM REVDAT 3 04-SEP-13 2V86 1 SOURCE REMARK VERSN REVDAT 2 24-FEB-09 2V86 1 VERSN REVDAT 1 11-DEC-07 2V86 0 JRNL AUTH S.RAMON-MAIQUES,A.J.KUO,D.CARNEY,A.G.W.MATTHEWS, JRNL AUTH 2 M.A.OETTINGER,O.GOZANI,W.YANG JRNL TITL THE PLANT HOMEODOMAIN FINGER OF RAG2 RECOGNIZES HISTONE H3 JRNL TITL 2 METHYLATED AT BOTH LYSINE-4 AND ARGININE-2. JRNL REF PROC.NATL.ACAD.SCI.USA V. 104 18993 2007 JRNL REFN ISSN 0027-8424 JRNL PMID 18025461 JRNL DOI 10.1073/PNAS.0709170104 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH A.G.W.MATTHEWS,A.J.KUO,S.RAMON-MAIQUES,S.HAN,K.S.CHAMPAGNE, REMARK 1 AUTH 2 D.IVANOV,M.GALLARDO,D.CARNEY,P.CHEUNG,D.N.CICCONE, REMARK 1 AUTH 3 K.L.WALTER,P.J.UTZ,Y.SHI,T.G.KUTATELADZE,W.YANG,O.GOZANI, REMARK 1 AUTH 4 M.A.OETTINGER REMARK 1 TITL RAG2 PHD FINGER COUPLES HISTONE H3 LYSINE 4 TRIMETHYLATION REMARK 1 TITL 2 WITH V(D)J RECOMBINATION. REMARK 1 REF NATURE V. 450 1106 2007 REMARK 1 REFN ISSN 0028-0836 REMARK 1 PMID 18033247 REMARK 1 DOI 10.1038/NATURE06431 REMARK 2 REMARK 2 RESOLUTION. 2.05 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.05 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 10000.000 REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 94.9 REMARK 3 NUMBER OF REFLECTIONS : 11257 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.173 REMARK 3 FREE R VALUE : 0.211 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 583 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.001 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 11 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.05 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.12 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.90 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 973 REMARK 3 BIN R VALUE (WORKING SET) : 0.2242 REMARK 3 BIN FREE R VALUE : 0.2909 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.00 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 49 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.040 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1448 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 4 REMARK 3 SOLVENT ATOMS : 329 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 18.50 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.50 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.13400 REMARK 3 B22 (A**2) : -0.12600 REMARK 3 B33 (A**2) : 0.26000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.21 REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 1.303 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.36 REMARK 3 BSOL : 47.24 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2V86 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 02-AUG-07. REMARK 100 THE DEPOSITION ID IS D_1290033367. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-MAR-06 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RU200 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU-MSC REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11827 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.050 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 5.000 REMARK 200 R MERGE (I) : 0.18000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.05 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.12 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 5.00 REMARK 200 R MERGE FOR SHELL (I) : 0.52000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 2V83 REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.48 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.23 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: VAPOR DIFFUSION. HANGING DROP. 28% PEG REMARK 280 20,000, 0.1M MES PH 6.5, 3% ISOPROPANOL TEMPERATURE 293K, VAPOR REMARK 280 DIFFUSION, HANGING DROP REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 43.74750 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 43.74750 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 31.45250 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 33.28450 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 31.45250 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 33.28450 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 43.74750 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 31.45250 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 33.28450 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 43.74750 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 31.45250 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 33.28450 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PQS REMARK 350 TOTAL BURIED SURFACE AREA: 1610 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7110 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -12.2 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, E REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PQS REMARK 350 TOTAL BURIED SURFACE AREA: 1500 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6990 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -12.2 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, D REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LEU A 408 CG CD1 CD2 REMARK 470 SER A 410 OG REMARK 470 LEU B 408 CG CD1 CD2 REMARK 470 ALA D 9 CA C O CB REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 CB LEU B 408 CB LEU B 408 4545 1.82 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 LEU A 408 -130.17 7.94 REMARK 500 PRO A 411 90.28 -22.59 REMARK 500 THR A 429 -12.86 -141.19 REMARK 500 PHE A 433 -60.88 -128.24 REMARK 500 LEU A 438 -68.52 -135.36 REMARK 500 TRP B 416 52.84 -104.01 REMARK 500 THR B 429 -16.06 -142.46 REMARK 500 PHE B 433 -61.58 -127.92 REMARK 500 LEU B 438 -69.78 -133.02 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A2125 DISTANCE = 5.93 ANGSTROMS REMARK 525 HOH B2150 DISTANCE = 5.86 ANGSTROMS REMARK 525 HOH B2158 DISTANCE = 7.87 ANGSTROMS REMARK 525 HOH E2003 DISTANCE = 6.26 ANGSTROMS REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A1488 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 419 SG REMARK 620 2 CYS A 423 SG 114.4 REMARK 620 3 HIS A 455 ND1 105.0 101.2 REMARK 620 4 CYS A 458 SG 111.8 109.2 114.9 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A1489 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 446 SG REMARK 620 2 HIS A 452 NE2 108.3 REMARK 620 3 CYS A 478 SG 118.7 109.6 REMARK 620 4 HIS A 481 ND1 119.2 101.0 98.5 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B1488 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 419 SG REMARK 620 2 CYS B 423 SG 116.4 REMARK 620 3 HIS B 455 ND1 107.9 103.5 REMARK 620 4 CYS B 458 SG 110.0 106.6 112.5 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B1489 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 446 SG REMARK 620 2 HIS B 452 NE2 102.0 REMARK 620 3 CYS B 478 SG 115.7 114.8 REMARK 620 4 HIS B 481 ND1 117.8 105.1 101.5 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 1488 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 1489 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 1488 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 1489 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2A23 RELATED DB: PDB REMARK 900 A PHD FINGER MOTIF IN THE C-TERMINUS OF RAG2 MODULATESRECOMBINATION REMARK 900 ACTIVITY REMARK 900 RELATED ID: 2V83 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF RAG2-PHD FINGER IN COMPLEX WITH H3K4ME3 PEPTIDE REMARK 900 RELATED ID: 2V85 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF RAG2-PHD FINGER IN COMPLEX WITH H3R2ME1K4ME3 REMARK 900 PEPTIDE REMARK 900 RELATED ID: 2V87 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF RAG2-PHD FINGER IN COMPLEX WITH H3R2ME2SK4ME3 REMARK 900 PEPTIDE REMARK 900 RELATED ID: 2V88 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF RAG2-PHD FINGER IN COMPLEX WITH H3R2ME2SK4ME2 REMARK 900 PEPTIDE REMARK 900 RELATED ID: 2V89 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF RAG2-PHD FINGER IN COMPLEX WITH H3K4ME3 REMARK 900 PEPTIDE AT 1.1A RESOLUTION REMARK 999 REMARK 999 SEQUENCE REMARK 999 N-TERMINAL SEGMENT GPLGSPEFG IS CARRIED OVER FROM THE REMARK 999 EXPRESSION VECTOR AFTER PROTEASE CLEAVAGE DBREF 2V86 A 414 487 UNP P21784 RAG2_MOUSE 414 487 DBREF 2V86 B 414 487 UNP P21784 RAG2_MOUSE 414 487 DBREF 2V86 D 1 9 UNP P84228 H32_MOUSE 2 10 DBREF 2V86 E 1 9 UNP P84228 H32_MOUSE 2 10 SEQADV 2V86 GLY A 406 UNP P21784 EXPRESSION TAG SEQADV 2V86 PRO A 407 UNP P21784 EXPRESSION TAG SEQADV 2V86 LEU A 408 UNP P21784 EXPRESSION TAG SEQADV 2V86 GLY A 409 UNP P21784 EXPRESSION TAG SEQADV 2V86 SER A 410 UNP P21784 EXPRESSION TAG SEQADV 2V86 PRO A 411 UNP P21784 EXPRESSION TAG SEQADV 2V86 GLU A 412 UNP P21784 EXPRESSION TAG SEQADV 2V86 PHE A 413 UNP P21784 EXPRESSION TAG SEQADV 2V86 GLY B 406 UNP P21784 EXPRESSION TAG SEQADV 2V86 PRO B 407 UNP P21784 EXPRESSION TAG SEQADV 2V86 LEU B 408 UNP P21784 EXPRESSION TAG SEQADV 2V86 GLY B 409 UNP P21784 EXPRESSION TAG SEQADV 2V86 SER B 410 UNP P21784 EXPRESSION TAG SEQADV 2V86 PRO B 411 UNP P21784 EXPRESSION TAG SEQADV 2V86 GLU B 412 UNP P21784 EXPRESSION TAG SEQADV 2V86 PHE B 413 UNP P21784 EXPRESSION TAG SEQADV 2V86 ALA D 9 UNP P84228 LYS 10 CONFLICT SEQADV 2V86 ALA E 9 UNP P84228 LYS 10 CONFLICT SEQRES 1 A 82 GLY PRO LEU GLY SER PRO GLU PHE GLY TYR TRP ILE THR SEQRES 2 A 82 CYS CYS PRO THR CYS ASP VAL ASP ILE ASN THR TRP VAL SEQRES 3 A 82 PRO PHE TYR SER THR GLU LEU ASN LYS PRO ALA MET ILE SEQRES 4 A 82 TYR CYS SER HIS GLY ASP GLY HIS TRP VAL HIS ALA GLN SEQRES 5 A 82 CYS MET ASP LEU GLU GLU ARG THR LEU ILE HIS LEU SER SEQRES 6 A 82 GLU GLY SER ASN LYS TYR TYR CYS ASN GLU HIS VAL GLN SEQRES 7 A 82 ILE ALA ARG ALA SEQRES 1 B 82 GLY PRO LEU GLY SER PRO GLU PHE GLY TYR TRP ILE THR SEQRES 2 B 82 CYS CYS PRO THR CYS ASP VAL ASP ILE ASN THR TRP VAL SEQRES 3 B 82 PRO PHE TYR SER THR GLU LEU ASN LYS PRO ALA MET ILE SEQRES 4 B 82 TYR CYS SER HIS GLY ASP GLY HIS TRP VAL HIS ALA GLN SEQRES 5 B 82 CYS MET ASP LEU GLU GLU ARG THR LEU ILE HIS LEU SER SEQRES 6 B 82 GLU GLY SER ASN LYS TYR TYR CYS ASN GLU HIS VAL GLN SEQRES 7 B 82 ILE ALA ARG ALA SEQRES 1 D 9 ALA DA2 THR M3L GLN THR ALA ARG ALA SEQRES 1 E 9 ALA DA2 THR M3L GLN THR ALA ARG ALA MODRES 2V86 DA2 D 2 ARG NG,NG-DIMETHYL-L-ARGININE MODRES 2V86 M3L D 4 LYS N-TRIMETHYLLYSINE MODRES 2V86 DA2 E 2 ARG NG,NG-DIMETHYL-L-ARGININE MODRES 2V86 M3L E 4 LYS N-TRIMETHYLLYSINE HET DA2 D 2 13 HET M3L D 4 12 HET DA2 E 2 26 HET M3L E 4 12 HET ZN A1488 1 HET ZN A1489 1 HET ZN B1488 1 HET ZN B1489 1 HETNAM DA2 NG,NG-DIMETHYL-L-ARGININE HETNAM M3L N-TRIMETHYLLYSINE HETNAM ZN ZINC ION HETSYN DA2 ADMA FORMUL 3 DA2 2(C8 H18 N4 O2) FORMUL 3 M3L 2(C9 H21 N2 O2 1+) FORMUL 5 ZN 4(ZN 2+) FORMUL 9 HOH *329(H2 O) HELIX 1 1 GLN A 457 ASP A 460 5 4 HELIX 2 2 GLU A 462 GLY A 472 1 11 HELIX 3 3 HIS A 481 ALA A 487 1 7 HELIX 4 4 GLN B 457 ASP B 460 5 4 HELIX 5 5 GLU B 462 GLY B 472 1 11 HELIX 6 6 HIS B 481 ALA B 487 1 7 SHEET 1 AA 2 MET A 443 CYS A 446 0 SHEET 2 AA 2 HIS A 452 HIS A 455 -1 O HIS A 452 N CYS A 446 SHEET 1 BA 2 MET B 443 CYS B 446 0 SHEET 2 BA 2 HIS B 452 HIS B 455 -1 O HIS B 452 N CYS B 446 LINK C ALA D 1 N DA2 D 2 1555 1555 1.33 LINK C DA2 D 2 N THR D 3 1555 1555 1.33 LINK C THR D 3 N M3L D 4 1555 1555 1.33 LINK C M3L D 4 N GLN D 5 1555 1555 1.33 LINK C ALA E 1 N BDA2 E 2 1555 1555 1.32 LINK C ALA E 1 N ADA2 E 2 1555 1555 1.33 LINK C BDA2 E 2 N THR E 3 1555 1555 1.33 LINK C ADA2 E 2 N THR E 3 1555 1555 1.33 LINK C THR E 3 N M3L E 4 1555 1555 1.33 LINK C M3L E 4 N GLN E 5 1555 1555 1.33 LINK SG CYS A 419 ZN ZN A1488 1555 1555 2.32 LINK SG CYS A 423 ZN ZN A1488 1555 1555 2.36 LINK SG CYS A 446 ZN ZN A1489 1555 1555 2.20 LINK NE2 HIS A 452 ZN ZN A1489 1555 1555 2.11 LINK ND1 HIS A 455 ZN ZN A1488 1555 1555 2.03 LINK SG CYS A 458 ZN ZN A1488 1555 1555 2.31 LINK SG CYS A 478 ZN ZN A1489 1555 1555 2.33 LINK ND1 HIS A 481 ZN ZN A1489 1555 1555 2.14 LINK SG CYS B 419 ZN ZN B1488 1555 1555 2.30 LINK SG CYS B 423 ZN ZN B1488 1555 1555 2.42 LINK SG CYS B 446 ZN ZN B1489 1555 1555 2.26 LINK NE2 HIS B 452 ZN ZN B1489 1555 1555 2.01 LINK ND1 HIS B 455 ZN ZN B1488 1555 1555 2.06 LINK SG CYS B 458 ZN ZN B1488 1555 1555 2.27 LINK SG CYS B 478 ZN ZN B1489 1555 1555 2.31 LINK ND1 HIS B 481 ZN ZN B1489 1555 1555 2.11 SITE 1 AC1 4 CYS A 419 CYS A 423 HIS A 455 CYS A 458 SITE 1 AC2 4 CYS A 446 HIS A 452 CYS A 478 HIS A 481 SITE 1 AC3 4 CYS B 419 CYS B 423 HIS B 455 CYS B 458 SITE 1 AC4 4 CYS B 446 HIS B 452 CYS B 478 HIS B 481 CRYST1 62.905 66.569 87.495 90.00 90.00 90.00 C 2 2 21 16 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.015897 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015022 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011429 0.00000