HEADER PROTEIN BINDING 02-AUG-07 2V83 TITLE CRYSTAL STRUCTURE OF RAG2-PHD FINGER IN COMPLEX WITH H3K4ME3 PEPTIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: VDJ RECOMBINATION-ACTIVATING PROTEIN 2; COMPND 3 CHAIN: A, B, C; 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: HISTONE H3; COMPND 9 CHAIN: D, E; COMPND 10 FRAGMENT: H3 (1-21), BIOTINILATED AT C-TERMINUS; COMPND 11 SYNONYM: H3K4ME3 PEPTIDE; COMPND 12 ENGINEERED: YES; COMPND 13 OTHER_DETAILS: 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_PLASMID: PGEX-6P-1; SOURCE 9 MOL_ID: 2; SOURCE 10 SYNTHETIC: YES; SOURCE 11 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 12 ORGANISM_COMMON: HUMAN; SOURCE 13 ORGANISM_TAXID: 9606 KEYWDS V(D)J RECOMBINATION, COVALENT MODIFICATIONS, RAG, HISTONE, NUCLEUS, KEYWDS 2 NUCLEASE, HYDROLASE, PHD FINGER, DNA-BINDING, RECOMBINASE, KEYWDS 3 ENDONUCLEASE, TRIMETYL LYSINE, DNA RECOMBINATION, PROTEIN BINDING EXPDTA X-RAY DIFFRACTION AUTHOR S.RAMON-MAIQUES,W.YANG REVDAT 7 06-FEB-19 2V83 1 REMARK REVDAT 6 30-JAN-19 2V83 1 REMARK REVDAT 5 28-DEC-16 2V83 1 COMPND SOURCE DBREF SEQADV REVDAT 4 10-OCT-12 2V83 1 REMARK VERSN FORMUL REVDAT 3 07-APR-09 2V83 1 REMARK REVDAT 2 24-FEB-09 2V83 1 VERSN REVDAT 1 11-DEC-07 2V83 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. 2.40 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 1.800 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 10178 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) : 0.196 REMARK 3 FREE R VALUE : 0.230 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.700 REMARK 3 FREE R VALUE TEST SET COUNT : 530 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.010 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 10 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.40 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.49 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 95.70 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 724 REMARK 3 BIN R VALUE (WORKING SET) : 0.2590 REMARK 3 BIN FREE R VALUE : 0.2193 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.50 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 34 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.038 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1937 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 6 REMARK 3 SOLVENT ATOMS : 234 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 30.50 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 30.50 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -5.54000 REMARK 3 B22 (A**2) : 3.81000 REMARK 3 B33 (A**2) : 1.73000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -1.81800 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL 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) : 0.007 REMARK 3 BOND ANGLES (DEGREES) : 1.504 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 : 40.21 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 2V83 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_1290033354. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-MAR-06; NULL REMARK 200 TEMPERATURE (KELVIN) : 95; NULL REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N; Y REMARK 200 RADIATION SOURCE : ROTATING ANODE; APS REMARK 200 BEAMLINE : NULL; 22-ID REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RU200; NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M; M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418; 1.2818 REMARK 200 MONOCHROMATOR : NULL; NULL REMARK 200 OPTICS : MIRRORS; NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE; CCD REMARK 200 DETECTOR MANUFACTURER : RIGAKU-MSC; MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11048 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.800 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 3.300 REMARK 200 R MERGE (I) : 0.15000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.49 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.7 REMARK 200 DATA REDUNDANCY IN SHELL : 2.50 REMARK 200 R MERGE FOR SHELL (I) : 0.49000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH; SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: PROTEIN MODEL DETERMINED BY SAD REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.68 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.18 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10% PEG 5000 MONOMETHYL ETHER, 0.1 M REMARK 280 BIS-TRIS PH 6.5 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K. REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 23.41750 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 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: PENTAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: PENTAMERIC REMARK 350 SOFTWARE USED: PQS REMARK 350 TOTAL BURIED SURFACE AREA: 4130 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 17680 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -30.2 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D, 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 GLY A 406 REMARK 465 PRO A 407 REMARK 465 LEU A 408 REMARK 465 GLY A 409 REMARK 465 SER A 410 REMARK 465 PRO A 411 REMARK 465 GLU A 412 REMARK 465 PHE A 413 REMARK 465 ARG A 486 REMARK 465 ALA A 487 REMARK 465 GLY B 406 REMARK 465 PRO B 407 REMARK 465 LEU B 408 REMARK 465 GLY C 406 REMARK 465 PRO C 407 REMARK 465 LEU C 408 REMARK 465 GLU C 471 REMARK 465 GLY C 472 REMARK 465 SER C 473 REMARK 465 ILE C 484 REMARK 465 ALA C 485 REMARK 465 ARG C 486 REMARK 465 ALA C 487 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 ILE A 484 CG1 CG2 CD1 REMARK 470 ALA A 485 CA C O CB REMARK 470 SER B 410 OG REMARK 470 GLN C 483 CA C O CB CG CD OE1 REMARK 470 GLN C 483 NE2 REMARK 470 ARG E 8 CG CD NE CZ NH1 NH2 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 TRP A 416 42.47 -97.59 REMARK 500 THR A 429 -11.12 -141.94 REMARK 500 LEU A 438 -73.17 -133.75 REMARK 500 SER B 410 108.90 73.26 REMARK 500 LEU B 438 -76.72 -124.62 REMARK 500 ALA B 485 108.78 -43.00 REMARK 500 ARG B 486 63.58 -105.69 REMARK 500 SER C 410 104.52 54.40 REMARK 500 CYS C 423 117.32 -33.42 REMARK 500 PHE C 433 -52.30 -124.64 REMARK 500 SER C 435 42.19 -72.55 REMARK 500 THR C 436 -14.85 -163.60 REMARK 500 LEU C 438 -82.38 -95.38 REMARK 500 HIS C 448 94.26 -62.44 REMARK 500 CYS C 478 171.39 -56.47 REMARK 500 VAL C 482 -118.10 -107.11 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 A2074 DISTANCE = 6.28 ANGSTROMS REMARK 525 HOH B2088 DISTANCE = 7.60 ANGSTROMS REMARK 525 HOH B2091 DISTANCE = 6.07 ANGSTROMS REMARK 525 HOH C2045 DISTANCE = 8.64 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 A1486 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 423 SG REMARK 620 2 HIS A 455 ND1 102.5 REMARK 620 3 CYS A 419 SG 111.4 101.2 REMARK 620 4 CYS A 458 SG 111.4 120.1 109.7 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A1487 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 452 NE2 REMARK 620 2 HIS A 481 ND1 102.3 REMARK 620 3 CYS A 446 SG 97.6 109.4 REMARK 620 4 CYS A 478 SG 118.7 111.2 116.1 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 109.6 REMARK 620 3 CYS B 458 SG 103.8 111.1 REMARK 620 4 HIS B 455 ND1 104.8 111.0 115.9 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 478 SG REMARK 620 2 HIS B 452 NE2 119.8 REMARK 620 3 CYS B 446 SG 115.6 102.4 REMARK 620 4 HIS B 481 ND1 96.0 106.6 116.9 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN C1484 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS C 458 SG REMARK 620 2 CYS C 419 SG 111.1 REMARK 620 3 HIS C 455 ND1 116.2 99.3 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN C1485 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS C 452 NE2 REMARK 620 2 CYS C 446 SG 114.4 REMARK 620 3 HIS C 481 ND1 111.9 101.3 REMARK 620 4 CYS C 478 SG 105.6 117.7 105.7 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 1486 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 1487 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 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN C 1484 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN C 1485 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: 2V85 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF RAG2-PHD FINGER IN COMPLEX WITH H3R2ME1K4ME3 REMARK 900 PEPTIDE REMARK 900 RELATED ID: 2V86 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF RAG2-PHD FINGER IN COMPLEX WITH H3R2ME2AK4ME3 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 ARE CARRIED OVER FROM THE REMARK 999 EXPRESSION VECTOR AFTER PROTEASE CLEAVAGE DBREF 2V83 A 414 487 UNP P21784 RAG2_MOUSE 414 487 DBREF 2V83 B 414 487 UNP P21784 RAG2_MOUSE 414 487 DBREF 2V83 C 414 487 UNP P21784 RAG2_MOUSE 414 487 DBREF 2V83 D 1 9 UNP Q5TEC6 Q5TEC6_HUMAN 2 10 DBREF 2V83 E 1 9 UNP Q5TEC6 Q5TEC6_HUMAN 2 10 SEQADV 2V83 GLY A 406 UNP P21784 EXPRESSION TAG SEQADV 2V83 PRO A 407 UNP P21784 EXPRESSION TAG SEQADV 2V83 LEU A 408 UNP P21784 EXPRESSION TAG SEQADV 2V83 GLY A 409 UNP P21784 EXPRESSION TAG SEQADV 2V83 SER A 410 UNP P21784 EXPRESSION TAG SEQADV 2V83 PRO A 411 UNP P21784 EXPRESSION TAG SEQADV 2V83 GLU A 412 UNP P21784 EXPRESSION TAG SEQADV 2V83 PHE A 413 UNP P21784 EXPRESSION TAG SEQADV 2V83 GLY B 406 UNP P21784 EXPRESSION TAG SEQADV 2V83 PRO B 407 UNP P21784 EXPRESSION TAG SEQADV 2V83 LEU B 408 UNP P21784 EXPRESSION TAG SEQADV 2V83 GLY B 409 UNP P21784 EXPRESSION TAG SEQADV 2V83 SER B 410 UNP P21784 EXPRESSION TAG SEQADV 2V83 PRO B 411 UNP P21784 EXPRESSION TAG SEQADV 2V83 GLU B 412 UNP P21784 EXPRESSION TAG SEQADV 2V83 PHE B 413 UNP P21784 EXPRESSION TAG SEQADV 2V83 GLY C 406 UNP P21784 EXPRESSION TAG SEQADV 2V83 PRO C 407 UNP P21784 EXPRESSION TAG SEQADV 2V83 LEU C 408 UNP P21784 EXPRESSION TAG SEQADV 2V83 GLY C 409 UNP P21784 EXPRESSION TAG SEQADV 2V83 SER C 410 UNP P21784 EXPRESSION TAG SEQADV 2V83 PRO C 411 UNP P21784 EXPRESSION TAG SEQADV 2V83 GLU C 412 UNP P21784 EXPRESSION TAG SEQADV 2V83 PHE C 413 UNP P21784 EXPRESSION TAG 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 C 82 GLY PRO LEU GLY SER PRO GLU PHE GLY TYR TRP ILE THR SEQRES 2 C 82 CYS CYS PRO THR CYS ASP VAL ASP ILE ASN THR TRP VAL SEQRES 3 C 82 PRO PHE TYR SER THR GLU LEU ASN LYS PRO ALA MET ILE SEQRES 4 C 82 TYR CYS SER HIS GLY ASP GLY HIS TRP VAL HIS ALA GLN SEQRES 5 C 82 CYS MET ASP LEU GLU GLU ARG THR LEU ILE HIS LEU SER SEQRES 6 C 82 GLU GLY SER ASN LYS TYR TYR CYS ASN GLU HIS VAL GLN SEQRES 7 C 82 ILE ALA ARG ALA SEQRES 1 D 9 ALA ARG THR M3L GLN THR ALA ARG LYS SEQRES 1 E 9 ALA ARG THR M3L GLN THR ALA ARG LYS MODRES 2V83 M3L D 4 LYS N-TRIMETHYLLYSINE MODRES 2V83 M3L E 4 LYS N-TRIMETHYLLYSINE HET M3L D 4 12 HET M3L E 4 12 HET ZN A1486 1 HET ZN A1487 1 HET ZN B1488 1 HET ZN B1489 1 HET ZN C1484 1 HET ZN C1485 1 HETNAM M3L N-TRIMETHYLLYSINE HETNAM ZN ZINC ION FORMUL 4 M3L 2(C9 H21 N2 O2 1+) FORMUL 6 ZN 6(ZN 2+) FORMUL 12 HOH *234(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 SER B 410 GLY B 414 5 5 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 GLN C 457 ASP C 460 5 4 HELIX 7 7 GLU C 462 SER C 470 1 9 SHEET 1 AA 3 HIS A 452 HIS A 455 0 SHEET 2 AA 3 MET A 443 CYS A 446 -1 O ILE A 444 N VAL A 454 SHEET 3 AA 3 THR D 3 M3L D 4 -1 O M3L D 4 N MET A 443 SHEET 1 BA 3 HIS B 452 HIS B 455 0 SHEET 2 BA 3 MET B 443 CYS B 446 -1 O ILE B 444 N VAL B 454 SHEET 3 BA 3 THR E 3 M3L E 4 -1 O M3L E 4 N MET B 443 SHEET 1 CA 2 MET C 443 CYS C 446 0 SHEET 2 CA 2 HIS C 452 HIS C 455 -1 O HIS C 452 N CYS C 446 LINK ZN ZN A1486 SG CYS A 423 1555 1555 2.42 LINK ZN ZN A1486 ND1 HIS A 455 1555 1555 2.09 LINK ZN ZN A1486 SG CYS A 419 1555 1555 2.29 LINK ZN ZN A1486 SG CYS A 458 1555 1555 2.32 LINK ZN ZN A1487 NE2 HIS A 452 1555 1555 1.96 LINK ZN ZN A1487 ND1 HIS A 481 1555 1555 2.12 LINK ZN ZN A1487 SG CYS A 446 1555 1555 2.22 LINK ZN ZN A1487 SG CYS A 478 1555 1555 2.28 LINK ZN ZN B1488 SG CYS B 419 1555 1555 2.31 LINK ZN ZN B1488 SG CYS B 423 1555 1555 2.30 LINK ZN ZN B1488 SG CYS B 458 1555 1555 2.25 LINK ZN ZN B1488 ND1 HIS B 455 1555 1555 1.97 LINK ZN ZN B1489 SG CYS B 478 1555 1555 2.32 LINK ZN ZN B1489 NE2 HIS B 452 1555 1555 2.00 LINK ZN ZN B1489 SG CYS B 446 1555 1555 2.32 LINK ZN ZN B1489 ND1 HIS B 481 1555 1555 2.04 LINK ZN ZN C1484 SG CYS C 458 1555 1555 2.25 LINK ZN ZN C1484 SG CYS C 419 1555 1555 2.36 LINK ZN ZN C1484 ND1 HIS C 455 1555 1555 1.95 LINK ZN ZN C1485 NE2 HIS C 452 1555 1555 2.07 LINK ZN ZN C1485 SG CYS C 446 1555 1555 2.15 LINK ZN ZN C1485 ND1 HIS C 481 1555 1555 2.21 LINK ZN ZN C1485 SG CYS C 478 1555 1555 2.40 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 THR E 3 N M3L E 4 1555 1555 1.33 LINK C M3L E 4 N GLN E 5 1555 1555 1.33 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 SITE 1 AC5 4 CYS C 419 CYS C 423 HIS C 455 CYS C 458 SITE 1 AC6 4 CYS C 446 HIS C 452 CYS C 478 HIS C 481 CRYST1 54.783 46.835 56.963 90.00 101.46 90.00 P 1 21 1 6 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 0.018254 0.000000 0.003700 0.00000 SCALE2 0.000000 0.021352 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017912 0.00000