10 20 30 40 50 60 70 80 2V87 - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER PROTEIN BINDING 02-AUG-07 2V87
TITLE CRYSTAL STRUCTURE OF RAG2-PHD FINGER IN COMPLEX WITH TITLE 2 H3R2ME2SK4ME3 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: HISTONE H3.2; COMPND 9 CHAIN: D, E; COMPND 10 SYNONYM: H3R2ME2SK4ME3 PEPTIDE; COMPND 11 FRAGMENT: H3 (1-21), BIOTINYLATED AT C-TERMINUS, UNP RESIDUES 2-14; COMPND 12 OTHER_DETAILS: SYMMETRIC DI-METHYLATED R2 AND TRI- COMPND 13 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_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, RAG, HISTONE, KEYWDS 2 NUCLEUS, NUCLEASE, HYDROLASE, PHD FINGER, DNA-BINDING, KEYWDS 3 RECOMBINASE, ENDONUCLEASE, SYMMETRIC DIMETHYLATED KEYWDS 4 ARGININE, PROTEIN BINDING, TRIMETHYL LYSINE, DNA KEYWDS 5 RECOMBINATION
EXPDTA X-RAY DIFFRACTION
AUTHOR S.RAMON-MAIQUES,W.YANG
REVDAT 4 08-FEB-17 2V87 1 COMPND SOURCE DBREF REVDAT 3 04-SEP-13 2V87 1 COMPND SOURCE REMARK VERSN REVDAT 3 2 FORMUL REVDAT 2 24-FEB-09 2V87 1 VERSN REVDAT 1 11-DEC-07 2V87 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 JRNL TITL 2 HISTONE H3 METHYLATED AT BOTH LYSINE-4 AND JRNL TITL 3 ARGININE-2. JRNL REF PROC.NAT.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. 1.8 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) : 1.8 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.0 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 10000 REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 93.5 REMARK 3 NUMBER OF REFLECTIONS : 18476 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) : 0.1810 REMARK 3 FREE R VALUE : 0.2081 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.6 REMARK 3 FREE R VALUE TEST SET COUNT : 908 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.0069 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 18 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.83 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 87.9 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 813 REMARK 3 BIN R VALUE (WORKING SET) : 0.3123 REMARK 3 BIN FREE R VALUE : 0.3336 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 3.6 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 30 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.061 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1380 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 54 REMARK 3 SOLVENT ATOMS : 237 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 27.2 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.18 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -8.762 REMARK 3 B22 (A**2) : 7.160 REMARK 3 B33 (A**2) : 1.602 REMARK 3 B12 (A**2) : 0.000 REMARK 3 B13 (A**2) : -1.737 REMARK 3 B23 (A**2) : 0.000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.184 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) : 0.007355 REMARK 3 BOND ANGLES (DEGREES) : 1.81092 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 : 0.344311 REMARK 3 BSOL : 46.7944 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 PARAMETER FILE 2 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4 REMARK 4 2V87 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 06-AUG-07. REMARK 100 THE PDBE ID CODE IS EBI-33369.
REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-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) : 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 : HKL2000 REMARK 200 DATA SCALING SOFTWARE : HKL2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19094 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.80 REMARK 200 RESOLUTION RANGE LOW (A) : 20.00 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.0 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.5 REMARK 200 DATA REDUNDANCY : 2.6 REMARK 200 R MERGE (I) : 0.06 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 25.50 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.86 REMARK 200 COMPLETENESS FOR SHELL (%) : 87.9 REMARK 200 DATA REDUNDANCY IN SHELL : 1.9 REMARK 200 R MERGE FOR SHELL (I) : 0.21 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.90 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 (%): 53.47 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.66 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: VAPOR DIFFUSION. HANGING DROP. REMARK 280 22% PEG 3350, 120-240 MM OF POTASSIUM FORMATE. TEMPERATURE REMARK 280 293K
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 23.31500 REMARK 290 SMTRY3 2 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: 1240 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 5690 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -8.4 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 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: 1250 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6390 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -8.3 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, 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 GLY B 406 REMARK 465 PRO B 407 REMARK 465 LEU B 408 REMARK 465 THR D 11 REMARK 465 GLY D 12 REMARK 465 GLY D 13
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 A 410 OG REMARK 470 ALA A 487 CA C O CB REMARK 470 SER B 410 OG REMARK 470 ARG D 8 CG CD NE CZ NH1 NH2 REMARK 470 LYS D 9 CG CD CE NZ REMARK 470 SER D 10 CA C O CB OG
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 O THR E 11 N GLY E 13 2.02 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 GLU A 412 CA GLU A 412 CB -0.167 REMARK 500 GLU A 412 CB GLU A 412 CG -0.165 REMARK 500 GLU A 412 CD GLU A 412 OE1 -0.115 REMARK 500 GLU A 412 CD GLU A 412 OE2 -0.116 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 LYS E 9 N - CA - C ANGL. DEV. = 26.8 DEGREES REMARK 500 SER E 10 N - CA - C ANGL. DEV. = -30.6 DEGREES REMARK 500 SER E 10 CA - C - N ANGL. DEV. = -15.8 DEGREES REMARK 500 THR E 11 C - N - CA ANGL. DEV. = 15.3 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 PRO A 411 -55.95 33.43 REMARK 500 PHE A 433 -52.94 -124.68 REMARK 500 LEU A 438 -69.16 -136.46 REMARK 500 LEU B 438 -81.01 -121.96 REMARK 500 SER E 10 -72.84 -164.39 REMARK 500 THR E 11 -79.51 62.44 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CHIRAL CENTERS REMARK 500 REMARK 500 UNEXPECTED CONFIGURATION OF THE FOLLOWING CHIRAL REMARK 500 CENTER(S) USING IMPROPER CA--C--CB--N CHIRALITY REMARK 500 FOR AMINO ACIDS AND C1'--O4'--N1(N9)--C2' FOR REMARK 500 NUCLEIC ACIDS OR EQUIVALENT ANGLE REMARK 500 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,A1,6X,F5.1,6X,A1,10X,A1,3X,A16) REMARK 500 REMARK 500 M RES CSSEQI IMPROPER EXPECTED FOUND DETAILS REMARK 500 GLU A 412 24.9 L L OUTSIDE RANGE REMARK 500 LYS E 9 18.7 L L OUTSIDE RANGE REMARK 500 SER E 10 47.6 L L OUTSIDE RANGE REMARK 500 REMARK 500 REMARK: NULL
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 A1487 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 458 SG REMARK 620 2 CYS A 423 SG 107.2 REMARK 620 3 HIS A 455 ND1 115.5 102.4 REMARK 620 4 CYS A 419 SG 111.4 117.4 102.9 REMARK 620 N 1 2 3 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 446 SG REMARK 620 2 HIS A 452 NE2 104.3 REMARK 620 3 CYS A 478 SG 116.1 113.8 REMARK 620 4 HIS A 481 ND1 121.5 100.2 100.2 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 423 SG REMARK 620 2 CYS B 419 SG 113.2 REMARK 620 3 HIS B 455 ND1 106.7 104.4 REMARK 620 4 CYS B 458 SG 110.0 110.3 112.1 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 HIS B 452 NE2 REMARK 620 2 HIS B 481 ND1 98.8 REMARK 620 3 CYS B 478 SG 111.6 99.1 REMARK 620 4 CYS B 446 SG 109.8 121.9 114.3 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 A1487 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A1488 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B1488 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B1489
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 REMARK 900 RAG2 MODULATESRECOMBINATION ACTIVITY REMARK 900 RELATED ID: 2V83 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF RAG2-PHD FINGER IN REMARK 900 COMPLEX WITH H3K4ME3 PEPTIDE REMARK 900 RELATED ID: 2V85 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF RAG2-PHD FINGER IN REMARK 900 COMPLEX WITH H3R2ME1K4ME3 PEPTIDE REMARK 900 RELATED ID: 2V86 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF RAG2-PHD FINGER IN REMARK 900 COMPLEX WITH H3R2ME2AK4ME3 PEPTIDE REMARK 900 RELATED ID: 2V88 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF RAG2-PHD FINGER IN REMARK 900 COMPLEX WITH H3R2ME2SK4ME2 PEPTIDE REMARK 900 RELATED ID: 2V89 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF RAG2-PHD FINGER IN REMARK 900 COMPLEX WITH H3K4ME3 PEPTIDE AT 1.1A REMARK 900 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 2V87 A 406 413 PDB 2V87 2V87 406 413 DBREF 2V87 A 414 487 UNP P21784 RAG2_MOUSE 414 487 DBREF 2V87 B 406 413 PDB 2V87 2V87 406 413 DBREF 2V87 B 414 487 UNP P21784 RAG2_MOUSE 414 487 DBREF 2V87 D 1 13 UNP P84228 H32_MOUSE 2 14 DBREF 2V87 E 1 13 UNP P84228 H32_MOUSE 2 14
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 13 ALA 2MR THR M3L GLN THR ALA ARG LYS SER THR GLY GLY SEQRES 1 E 13 ALA 2MR THR M3L GLN THR ALA ARG LYS SER THR GLY GLY
MODRES 2V87 M3L D 4 LYS N-TRIMETHYLLYSINE MODRES 2V87 2MR E 2 ARG N3, N4-DIMETHYLARGININE MODRES 2V87 M3L E 4 LYS N-TRIMETHYLLYSINE MODRES 2V87 2MR D 2 ARG N3, N4-DIMETHYLARGININE
HET ZN A1487 1 HET ZN A1488 1 HET 2MR D 2 13 HET M3L D 4 12 HET 2MR E 2 13 HET M3L E 4 12 HET ZN B1488 1 HET ZN B1489 1
HETNAM M3L N-TRIMETHYLLYSINE HETNAM 2MR N3, N4-DIMETHYLARGININE HETNAM ZN ZINC ION
FORMUL 5 M3L 2(C9 H21 N2 O2 1+) FORMUL 6 2MR 2(C8 H18 N4 O2) FORMUL 7 ZN 4(ZN 2+) FORMUL 8 HOH *237(H2 O)
HELIX 1 1 GLN A 457 ASP A 460 5 4 HELIX 2 2 GLU A 462 GLU A 471 1 10 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
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
LINK ZN ZN A1487 SG CYS A 458 1555 1555 2.31 LINK ZN ZN A1487 SG CYS A 423 1555 1555 2.31 LINK ZN ZN A1487 ND1 HIS A 455 1555 1555 2.13 LINK ZN ZN A1487 SG CYS A 419 1555 1555 2.29 LINK ZN ZN A1488 SG CYS A 446 1555 1555 2.24 LINK ZN ZN A1488 NE2 HIS A 452 1555 1555 2.01 LINK ZN ZN A1488 SG CYS A 478 1555 1555 2.31 LINK ZN ZN A1488 ND1 HIS A 481 1555 1555 2.15 LINK ZN ZN B1488 ND1 HIS B 455 1555 1555 2.16 LINK ZN ZN B1488 SG CYS B 458 1555 1555 2.28 LINK ZN ZN B1488 SG CYS B 423 1555 1555 2.36 LINK ZN ZN B1488 SG CYS B 419 1555 1555 2.32 LINK ZN ZN B1489 SG CYS B 446 1555 1555 2.31 LINK ZN ZN B1489 NE2 HIS B 452 1555 1555 2.12 LINK ZN ZN B1489 ND1 HIS B 481 1555 1555 2.10 LINK ZN ZN B1489 SG CYS B 478 1555 1555 2.26 LINK C ALA D 1 N 2MR D 2 1555 1555 1.33 LINK C 2MR 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 2MR E 2 1555 1555 1.32 LINK C 2MR 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
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 40.407 46.630 57.005 90.00 95.13 90.00 P 1 21 1 4
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 0.024748 0.000000 0.002222 0.00000
SCALE2 0.000000 0.021445 0.000000 0.00000
SCALE3 0.000000 0.000000 0.017613 0.00000