HEADER PROTEIN BINDING 03-AUG-07 2V89 TITLE CRYSTAL STRUCTURE OF RAG2-PHD FINGER IN COMPLEX WITH H3K4ME3 PEPTIDE TITLE 2 AT 1.1A RESOLUTION 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: HISTONE H3; COMPND 9 CHAIN: D, E; COMPND 10 FRAGMENT: H3 (1-21), BIOTINYLATED AT C-TERMINUS; COMPND 11 SYNONYM: H3K4ME3 PEPTIDE; COMPND 12 ENGINEERED: YES; COMPND 13 OTHER_DETAILS: TRI-METHYLATED K4 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, TRIMETHYL LYSINE, DNA RECOMBINATION, PROTEIN BINDING EXPDTA X-RAY DIFFRACTION AUTHOR S.RAMON-MAIQUES,W.YANG REVDAT 7 13-DEC-23 2V89 1 REMARK LINK ATOM REVDAT 6 08-MAY-19 2V89 1 REMARK REVDAT 5 06-MAR-19 2V89 1 REMARK LINK REVDAT 4 28-DEC-16 2V89 1 COMPND SOURCE REMARK DBREF REVDAT 4 2 1 SEQADV REVDAT 3 13-MAR-13 2V89 1 COMPND JRNL REMARK VERSN REVDAT 3 2 1 FORMUL REVDAT 2 24-FEB-09 2V89 1 VERSN REVDAT 1 11-DEC-07 2V89 0 JRNL AUTH A.G.W.MATTHEWS,A.J.KUO,S.RAMON-MAIQUES,S.HAN,K.S.CHAMPAGNE, JRNL AUTH 2 D.IVANOV,M.GALLARDO,D.CARNEY,P.CHEUNG,D.N.CICCONE, JRNL AUTH 3 K.L.WALTER,P.J.UTZ,Y.SHI,T.G.KUTATELADZE,W.YANG,O.GOZANI, JRNL AUTH 4 M.A.OETTINGER JRNL TITL RAG2 PHD FINGER COUPLES HISTONE H3 LYSINE 4 TRIMETHYLATION JRNL TITL 2 WITH V(D)J RECOMBINATION. JRNL REF NATURE V. 450 1106 2007 JRNL REFN ISSN 0028-0836 JRNL PMID 18033247 JRNL DOI 10.1038/NATURE06431 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH S.RAMON-MAIQUES,A.J.KUO,D.CARNEY,A.G.W.MATTHEWS, REMARK 1 AUTH 2 M.A.OETTINGER,O.GOZANI,W.YANG REMARK 1 TITL THE PLANT HOMEODOMAIN FINGER OF RAG2 RECOGNIZES HISTONE H3 REMARK 1 TITL 2 METHYLATED AT BOTH LYSINE-4 AND ARGININE-2. REMARK 1 REF PROC.NATL.ACAD.SCI.USA V. 104 18993 2007 REMARK 1 REFN ISSN 0027-8424 REMARK 1 PMID 18025461 REMARK 1 DOI 10.1073/PNAS.0709170104 REMARK 2 REMARK 2 RESOLUTION. 1.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELXL-97 REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 1.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 93.8 REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.123 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.155 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 4.600 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 3493 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 75608 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : NULL REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : 0.108 REMARK 3 FREE R VALUE (F>4SIG(F)) : 0.144 REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : 2693 REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 55307 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1373 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 4 REMARK 3 SOLVENT ATOMS : 319 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 1651.2 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 1233.3 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 6 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 15567 REMARK 3 NUMBER OF RESTRAINTS : 18875 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.016 REMARK 3 ANGLE DISTANCES (A) : 0.033 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.000 REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.031 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.086 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.091 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.030 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.006 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.054 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.114 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: NULL REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH AND HUBER REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: ANISOTROPIC SCALING APPLIED BY THE REMARK 3 METHOD OF PARKIN, MOEZZI & HOPE, J.APPL.CRYST.28(1995)53-56 REMARK 4 REMARK 4 2V89 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 03-AUG-07. REMARK 100 THE DEPOSITION ID IS D_1290033376. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-AUG-06 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 22-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 75608 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.100 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.8 REMARK 200 DATA REDUNDANCY : 3.600 REMARK 200 R MERGE (I) : 0.06000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 28.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.14 REMARK 200 COMPLETENESS FOR SHELL (%) : 67.5 REMARK 200 DATA REDUNDANCY IN SHELL : 2.90 REMARK 200 R MERGE FOR SHELL (I) : 0.36000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.400 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 (%): 44.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.21 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: CRYSTALS OF COMPLEX WERE OBTAINED AT 3 REMARK 280 MG/ML PROTEIN CONCENTRATION AND 1:1.5 MOLAR RATIO OF PROTEIN TO REMARK 280 PEPTIDE USING HANGING DROP AND VAPOR DIFFUSION TECHNIQUE AT REMARK 280 293K. PRECIPITANT SOLUTION: 26% PEG 3350, 0.18M POTASSIUM REMARK 280 THIOCYANATE., VAPOR DIFFUSION, HANGING DROP REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z REMARK 290 4555 -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 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 37.98900 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 23.40350 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 37.98900 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 23.40350 REMARK 290 SMTRY3 4 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: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1090 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6150 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -7.8 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: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1200 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 5630 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -8.2 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 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 1406 REMARK 465 PRO A 1407 REMARK 465 LEU A 1408 REMARK 465 GLY A 1409 REMARK 465 GLY B 406 REMARK 465 PRO B 407 REMARK 465 LEU B 408 REMARK 465 GLY B 409 REMARK 465 SER B 410 REMARK 465 PRO B 411 REMARK 465 GLU B 412 REMARK 465 PHE B 413 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 SER A1410 OG REMARK 470 GLU A1412 CG CD OE1 OE2 REMARK 470 ALA B 487 CA C O CB REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 HD1 HIS A 1481 ZN ZN A 2489 1.21 REMARK 500 HD1 HIS A 1455 ZN ZN A 2488 1.22 REMARK 500 HD1 HIS B 455 ZN ZN B 1488 1.22 REMARK 500 HD1 HIS B 481 ZN ZN B 1489 1.24 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 PRO A1411 C - N - CA ANGL. DEV. = 9.6 DEGREES REMARK 500 TYR A1415 CB - CG - CD2 ANGL. DEV. = -4.3 DEGREES REMARK 500 GLU A1462 OE1 - CD - OE2 ANGL. DEV. = 7.8 DEGREES REMARK 500 ARG A1464 NE - CZ - NH2 ANGL. DEV. = -3.5 DEGREES REMARK 500 ARG A1486 NE - CZ - NH2 ANGL. DEV. = -5.2 DEGREES REMARK 500 ASP B 460 CB - CG - OD1 ANGL. DEV. = 6.2 DEGREES REMARK 500 ARG B 464 NE - CZ - NH1 ANGL. DEV. = 4.4 DEGREES REMARK 500 LYS B 475 CB - CG - CD ANGL. DEV. = 16.6 DEGREES REMARK 500 ARG B 486 NE - CZ - NH2 ANGL. DEV. = 5.2 DEGREES REMARK 500 ARG D3002 NE - CZ - NH2 ANGL. DEV. = -3.7 DEGREES 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 GLU A1412 -174.84 5.32 REMARK 500 PHE A1413 -72.56 71.27 REMARK 500 PHE A1433 -46.56 -130.78 REMARK 500 LEU A1438 -82.29 -117.45 REMARK 500 PHE B 433 -53.32 -126.53 REMARK 500 LEU B 438 -64.47 -139.55 REMARK 500 ARG B 486 -11.79 -151.37 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 PRO A 1411 GLU A 1412 116.38 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 B2001 DISTANCE = 6.69 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 A2488 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A1419 SG REMARK 620 2 CYS A1423 SG 115.4 REMARK 620 3 HIS A1455 ND1 102.6 106.0 REMARK 620 4 CYS A1458 SG 111.0 110.2 111.3 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A2489 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A1446 SG REMARK 620 2 HIS A1452 NE2 106.0 REMARK 620 3 CYS A1478 SG 114.8 112.4 REMARK 620 4 HIS A1481 ND1 120.9 100.3 101.7 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 116.6 REMARK 620 3 HIS B 455 ND1 101.7 104.4 REMARK 620 4 CYS B 458 SG 110.9 109.1 114.0 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 105.4 REMARK 620 3 CYS B 478 SG 116.6 111.6 REMARK 620 4 HIS B 481 ND1 119.2 102.0 101.2 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 2488 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 2489 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: 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: 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: 2V88 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF RAG2-PHD FINGER IN COMPLEX WITH H3R2ME2SK4ME2 REMARK 900 PEPTIDE REMARK 999 REMARK 999 SEQUENCE REMARK 999 N-TERMINAL SEGMENT GPLGSPEFG IS CARRIED OVER FROM THE REMARK 999 EXPRESSION VECTOR AFTER PROTEASE CLEAVAGE DBREF 2V89 A 1414 1487 UNP P21784 RAG2_MOUSE 414 487 DBREF 2V89 B 414 487 UNP P21784 RAG2_MOUSE 414 487 DBREF 2V89 D 3001 3010 UNP Q5TEC6 Q5TEC6_HUMAN 2 10 DBREF 2V89 E 2001 2010 UNP Q5TEC6 Q5TEC6_HUMAN 2 10 SEQADV 2V89 GLY A 1406 UNP P21784 EXPRESSION TAG SEQADV 2V89 PRO A 1407 UNP P21784 EXPRESSION TAG SEQADV 2V89 LEU A 1408 UNP P21784 EXPRESSION TAG SEQADV 2V89 GLY A 1409 UNP P21784 EXPRESSION TAG SEQADV 2V89 SER A 1410 UNP P21784 EXPRESSION TAG SEQADV 2V89 PRO A 1411 UNP P21784 EXPRESSION TAG SEQADV 2V89 GLU A 1412 UNP P21784 EXPRESSION TAG SEQADV 2V89 PHE A 1413 UNP P21784 EXPRESSION TAG SEQADV 2V89 GLY B 406 UNP P21784 EXPRESSION TAG SEQADV 2V89 PRO B 407 UNP P21784 EXPRESSION TAG SEQADV 2V89 LEU B 408 UNP P21784 EXPRESSION TAG SEQADV 2V89 GLY B 409 UNP P21784 EXPRESSION TAG SEQADV 2V89 SER B 410 UNP P21784 EXPRESSION TAG SEQADV 2V89 PRO B 411 UNP P21784 EXPRESSION TAG SEQADV 2V89 GLU B 412 UNP P21784 EXPRESSION TAG SEQADV 2V89 PHE B 413 UNP P21784 EXPRESSION TAG SEQADV 2V89 ALA D 3008 UNP Q5TEC6 ARG 9 CONFLICT SEQADV 2V89 ALA D 3010 UNP Q5TEC6 SER 10 CONFLICT SEQADV 2V89 ALA E 2008 UNP Q5TEC6 ARG 9 CONFLICT SEQADV 2V89 ALA E 2010 UNP Q5TEC6 SER 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 10 ALA ARG THR M3L GLN THR ALA ALA LYS ALA SEQRES 1 E 10 ALA ARG THR M3L GLN THR ALA ALA LYS ALA MODRES 2V89 M3L D 3004 LYS N-TRIMETHYLLYSINE MODRES 2V89 M3L E 2004 LYS N-TRIMETHYLLYSINE HET M3L D3004 31 HET M3L E2004 31 HET ZN A2488 1 HET ZN A2489 1 HET ZN B1488 1 HET ZN B1489 1 HETNAM M3L N-TRIMETHYLLYSINE HETNAM ZN ZINC ION FORMUL 3 M3L 2(C9 H21 N2 O2 1+) FORMUL 5 ZN 4(ZN 2+) FORMUL 9 HOH *319(H2 O) HELIX 1 1 SER A 1410 GLY A 1414 5 5 HELIX 2 2 GLN A 1457 ASP A 1460 5 4 HELIX 3 3 GLU A 1462 GLY A 1472 1 11 HELIX 4 4 GLN B 457 ASP B 460 5 4 HELIX 5 5 GLU B 462 GLU B 471 1 10 SHEET 1 AA 3 HIS A1452 HIS A1455 0 SHEET 2 AA 3 MET A1443 CYS A1446 -1 O ILE A1444 N VAL A1454 SHEET 3 AA 3 THR E2003 M3L E2004 -1 O M3L E2004 N MET A1443 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 D3003 M3L D3004 -1 O M3L D3004 N MET B 443 LINK C THR D3003 N M3L D3004 1555 1555 1.34 LINK C M3L D3004 N GLN D3005 1555 1555 1.32 LINK C THR E2003 N M3L E2004 1555 1555 1.33 LINK C M3L E2004 N GLN E2005 1555 1555 1.31 LINK SG CYS A1419 ZN ZN A2488 1555 1555 2.32 LINK SG CYS A1423 ZN ZN A2488 1555 1555 2.31 LINK SG CYS A1446 ZN ZN A2489 1555 1555 2.29 LINK NE2 HIS A1452 ZN ZN A2489 1555 1555 2.01 LINK ND1 HIS A1455 ZN ZN A2488 1555 1555 2.07 LINK SG CYS A1458 ZN ZN A2488 1555 1555 2.32 LINK SG CYS A1478 ZN ZN A2489 1555 1555 2.32 LINK ND1 HIS A1481 ZN ZN A2489 1555 1555 2.03 LINK SG CYS B 419 ZN ZN B1488 1555 1555 2.30 LINK SG CYS B 423 ZN ZN B1488 1555 1555 2.31 LINK SG CYS B 446 ZN ZN B1489 1555 1555 2.30 LINK NE2 HIS B 452 ZN ZN B1489 1555 1555 2.02 LINK ND1 HIS B 455 ZN ZN B1488 1555 1555 2.08 LINK SG CYS B 458 ZN ZN B1488 1555 1555 2.32 LINK SG CYS B 478 ZN ZN B1489 1555 1555 2.29 LINK ND1 HIS B 481 ZN ZN B1489 1555 1555 2.06 SITE 1 AC1 4 CYS A1419 CYS A1423 HIS A1455 CYS A1458 SITE 1 AC2 4 CYS A1446 HIS A1452 CYS A1478 HIS A1481 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 75.978 46.807 56.808 90.00 106.78 90.00 C 1 2 1 8 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 0.013162 0.000000 0.003969 0.00000 SCALE2 0.000000 0.021364 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018386 0.00000