PDB Short entry for 3GNB HEADER RECOMBINATION 16-MAR-09 3GNB TITLE CRYSTAL STRUCTURE OF THE RAG1 NONAMER-BINDING DOMAIN WITH DNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: V(D)J RECOMBINATION-ACTIVATING PROTEIN 1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: NONAMER BINDING DOMAIN: UNP RESIDUES 389-456; COMPND 5 SYNONYM: RAG-1; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: 5'-D(*AP*AP*TP*TP*TP*TP*CP*AP*GP*AP*AP*AP*CP*C)-3'; COMPND 9 CHAIN: D; COMPND 10 ENGINEERED: YES; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: 5'-D(*AP*GP*GP*TP*TP*TP*CP*TP*GP*AP*AP*AP*AP*C)-3'; COMPND 13 CHAIN: E; COMPND 14 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 GENE: RAG1, RAG-1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET28A; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 MOL_ID: 3; SOURCE 14 SYNTHETIC: YES KEYWDS VDJ RECOMBINATION, DNA RECOMBINATION, DNA-BINDING, ENDONUCLEASE, KEYWDS 2 HYDROLASE, METAL-BINDING, NUCLEASE, NUCLEUS, ZINC-FINGER, KEYWDS 3 RECOMBINATION EXPDTA X-RAY DIFFRACTION AUTHOR F.F.YIN,S.BAILEY,C.A.INNIS,T.A.STEITZ,D.G.SCHATZ REVDAT 4 06-SEP-23 3GNB 1 SEQADV REVDAT 3 13-JUL-11 3GNB 1 VERSN REVDAT 2 19-MAY-09 3GNB 1 JRNL REVDAT 1 28-APR-09 3GNB 0 JRNL AUTH F.F.YIN,S.BAILEY,C.A.INNIS,M.CIUBOTARU,S.KAMTEKAR, JRNL AUTH 2 T.A.STEITZ,D.G.SCHATZ JRNL TITL STRUCTURE OF THE RAG1 NONAMER BINDING DOMAIN WITH DNA JRNL TITL 2 REVEALS A DIMER THAT MEDIATES DNA SYNAPSIS. JRNL REF NAT.STRUCT.MOL.BIOL. V. 16 499 2009 JRNL REFN ISSN 1545-9993 JRNL PMID 19396172 JRNL DOI 10.1038/NSMB.1593 REMARK 2 REMARK 2 RESOLUTION. 3.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 3382 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 + TEST SET) : 0.243 REMARK 3 R VALUE (WORKING SET) : 0.242 REMARK 3 FREE R VALUE : 0.267 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.500 REMARK 3 FREE R VALUE TEST SET COUNT : 158 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 3.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.08 REMARK 3 REFLECTION IN BIN (WORKING SET) : 235 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.3320 REMARK 3 BIN FREE R VALUE SET COUNT : 10 REMARK 3 BIN FREE R VALUE : 0.4410 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 553 REMARK 3 NUCLEIC ACID ATOMS : 548 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 8 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 46.72 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.36000 REMARK 3 B22 (A**2) : 0.36000 REMARK 3 B33 (A**2) : -0.72000 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 OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.468 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.377 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 52.263 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.936 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.915 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1175 ; 0.005 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): 670 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1691 ; 1.071 ; 2.547 REMARK 3 BOND ANGLES OTHERS (DEGREES): 1647 ; 0.899 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 69 ; 3.592 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 30 ;23.445 ;22.333 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 117 ;15.234 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 9 ;11.679 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 191 ; 0.053 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 890 ; 0.002 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 119 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 144 ; 0.222 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 567 ; 0.186 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 437 ; 0.209 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 422 ; 0.082 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 17 ; 0.058 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 12 ; 0.144 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 59 ; 0.232 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 2 ; 0.163 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 451 ; 0.090 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 139 ; 0.016 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 538 ; 0.112 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1137 ; 0.082 ; 2.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1152 ; 0.120 ; 2.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : 1 REMARK 3 REMARK 3 NCS GROUP NUMBER : 1 REMARK 3 CHAIN NAMES : D E REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 1 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 1 D 1 D 14 3 REMARK 3 1 E 1 E 14 3 REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 LOOSE POSITIONAL 1 D (A): 280 ; 0.17 ; NULL REMARK 3 LOOSE THERMAL 1 D (A**2): 280 ; 0.21 ; 10.00 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : D 1 D 14 REMARK 3 RESIDUE RANGE : E 1 E 14 REMARK 3 ORIGIN FOR THE GROUP (A): 48.7124 13.6212 -0.0282 REMARK 3 T TENSOR REMARK 3 T11: 0.2620 T22: 0.1139 REMARK 3 T33: -0.0628 T12: 0.5879 REMARK 3 T13: 0.0622 T23: -0.0206 REMARK 3 L TENSOR REMARK 3 L11: 8.6225 L22: 5.0028 REMARK 3 L33: 5.3068 L12: -1.0279 REMARK 3 L13: -0.2527 L23: 5.1156 REMARK 3 S TENSOR REMARK 3 S11: 0.5263 S12: -1.3833 S13: -0.9934 REMARK 3 S21: 0.5772 S22: -0.1789 S23: 0.4436 REMARK 3 S31: -0.1616 S32: 1.0468 S33: -0.3474 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 389 A 456 REMARK 3 ORIGIN FOR THE GROUP (A): 28.1235 24.0105 -0.8618 REMARK 3 T TENSOR REMARK 3 T11: 0.0706 T22: -0.0456 REMARK 3 T33: -0.2479 T12: 0.0369 REMARK 3 T13: -0.0420 T23: 0.0849 REMARK 3 L TENSOR REMARK 3 L11: 7.1005 L22: 4.8455 REMARK 3 L33: 6.8334 L12: -2.9627 REMARK 3 L13: -2.5106 L23: 2.0630 REMARK 3 S TENSOR REMARK 3 S11: -0.0785 S12: -0.3068 S13: -0.5948 REMARK 3 S21: 0.4106 S22: 0.1561 S23: 0.1653 REMARK 3 S31: 0.3030 S32: 0.2300 S33: -0.0776 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: 1. THE BIJVOET PAIRS WERE USED IN REMARK 3 PHASING. 2. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS REMARK 4 REMARK 4 3GNB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 31-MAR-09. REMARK 100 THE DEPOSITION ID IS D_1000052074. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-JUN-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 24-ID-C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.008 REMARK 200 MONOCHROMATOR : SI(111) CHANNEL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 3382 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.000 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 (%) : 99.2 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.06600 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.11 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.23900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: REFMAC 5.2.0019 REMARK 200 STARTING MODEL: PDB ENTRY 3GNA REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.54 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.14 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG 400, PH 7.5, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 4 2 2 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 -Y,X,Z REMARK 290 4555 Y,-X,Z REMARK 290 5555 -X,Y,-Z REMARK 290 6555 X,-Y,-Z REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z REMARK 290 9555 X+1/2,Y+1/2,Z+1/2 REMARK 290 10555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 11555 -Y+1/2,X+1/2,Z+1/2 REMARK 290 12555 Y+1/2,-X+1/2,Z+1/2 REMARK 290 13555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 14555 X+1/2,-Y+1/2,-Z+1/2 REMARK 290 15555 Y+1/2,X+1/2,-Z+1/2 REMARK 290 16555 -Y+1/2,-X+1/2,-Z+1/2 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 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 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 0.00000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 1.000000 0.000000 0.000000 48.73500 REMARK 290 SMTRY2 9 0.000000 1.000000 0.000000 48.73500 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 34.89000 REMARK 290 SMTRY1 10 -1.000000 0.000000 0.000000 48.73500 REMARK 290 SMTRY2 10 0.000000 -1.000000 0.000000 48.73500 REMARK 290 SMTRY3 10 0.000000 0.000000 1.000000 34.89000 REMARK 290 SMTRY1 11 0.000000 -1.000000 0.000000 48.73500 REMARK 290 SMTRY2 11 1.000000 0.000000 0.000000 48.73500 REMARK 290 SMTRY3 11 0.000000 0.000000 1.000000 34.89000 REMARK 290 SMTRY1 12 0.000000 1.000000 0.000000 48.73500 REMARK 290 SMTRY2 12 -1.000000 0.000000 0.000000 48.73500 REMARK 290 SMTRY3 12 0.000000 0.000000 1.000000 34.89000 REMARK 290 SMTRY1 13 -1.000000 0.000000 0.000000 48.73500 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 48.73500 REMARK 290 SMTRY3 13 0.000000 0.000000 -1.000000 34.89000 REMARK 290 SMTRY1 14 1.000000 0.000000 0.000000 48.73500 REMARK 290 SMTRY2 14 0.000000 -1.000000 0.000000 48.73500 REMARK 290 SMTRY3 14 0.000000 0.000000 -1.000000 34.89000 REMARK 290 SMTRY1 15 0.000000 1.000000 0.000000 48.73500 REMARK 290 SMTRY2 15 1.000000 0.000000 0.000000 48.73500 REMARK 290 SMTRY3 15 0.000000 0.000000 -1.000000 34.89000 REMARK 290 SMTRY1 16 0.000000 -1.000000 0.000000 48.73500 REMARK 290 SMTRY2 16 -1.000000 0.000000 0.000000 48.73500 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 34.89000 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: HEXAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 350 BIOMT1 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 6 LIES ON A SPECIAL POSITION. 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 MET A 369 REMARK 465 GLY A 370 REMARK 465 SER A 371 REMARK 465 SER A 372 REMARK 465 HIS A 373 REMARK 465 HIS A 374 REMARK 465 HIS A 375 REMARK 465 HIS A 376 REMARK 465 HIS A 377 REMARK 465 HIS A 378 REMARK 465 SER A 379 REMARK 465 SER A 380 REMARK 465 GLY A 381 REMARK 465 LEU A 382 REMARK 465 VAL A 383 REMARK 465 PRO A 384 REMARK 465 GLY A 385 REMARK 465 SER A 386 REMARK 465 HIS A 387 REMARK 465 MET A 388 REMARK 465 GLY A 457 REMARK 465 ARG A 458 REMARK 465 GLY A 459 REMARK 465 SER A 460 REMARK 465 GLY A 461 REMARK 465 LEU A 462 REMARK 465 GLN A 463 REMARK 465 PRO A 464 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 DA D 1 N9 C8 N7 C5 C6 N6 N1 REMARK 470 DA D 1 C2 N3 C4 REMARK 470 DA E 1 N9 C8 N7 C5 C6 N6 N1 REMARK 470 DA E 1 C2 N3 C4 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 DT D 3 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 DC D 13 O4' - C4' - C3' ANGL. DEV. = -3.3 DEGREES REMARK 500 DC D 13 O4' - C1' - N1 ANGL. DEV. = 5.1 DEGREES REMARK 500 DA E 10 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES REMARK 500 DA E 13 O4' - C4' - C3' ANGL. DEV. = -3.8 DEGREES REMARK 500 DA E 13 O4' - C1' - N9 ANGL. DEV. = 3.9 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 ARG A 409 -51.21 -29.38 REMARK 500 GLU A 444 58.57 -101.31 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3GNA RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE RAG1 NONAMER-BINDING DOMAIN WITH DNA DBREF 3GNB A 389 464 UNP P15919 RAG1_MOUSE 389 464 DBREF 3GNB D 1 14 PDB 3GNB 3GNB 1 14 DBREF 3GNB E 1 14 PDB 3GNB 3GNB 1 14 SEQADV 3GNB MET A 369 UNP P15919 EXPRESSION TAG SEQADV 3GNB GLY A 370 UNP P15919 EXPRESSION TAG SEQADV 3GNB SER A 371 UNP P15919 EXPRESSION TAG SEQADV 3GNB SER A 372 UNP P15919 EXPRESSION TAG SEQADV 3GNB HIS A 373 UNP P15919 EXPRESSION TAG SEQADV 3GNB HIS A 374 UNP P15919 EXPRESSION TAG SEQADV 3GNB HIS A 375 UNP P15919 EXPRESSION TAG SEQADV 3GNB HIS A 376 UNP P15919 EXPRESSION TAG SEQADV 3GNB HIS A 377 UNP P15919 EXPRESSION TAG SEQADV 3GNB HIS A 378 UNP P15919 EXPRESSION TAG SEQADV 3GNB SER A 379 UNP P15919 EXPRESSION TAG SEQADV 3GNB SER A 380 UNP P15919 EXPRESSION TAG SEQADV 3GNB GLY A 381 UNP P15919 EXPRESSION TAG SEQADV 3GNB LEU A 382 UNP P15919 EXPRESSION TAG SEQADV 3GNB VAL A 383 UNP P15919 EXPRESSION TAG SEQADV 3GNB PRO A 384 UNP P15919 EXPRESSION TAG SEQADV 3GNB GLY A 385 UNP P15919 EXPRESSION TAG SEQADV 3GNB SER A 386 UNP P15919 EXPRESSION TAG SEQADV 3GNB HIS A 387 UNP P15919 EXPRESSION TAG SEQADV 3GNB MET A 388 UNP P15919 EXPRESSION TAG SEQRES 1 A 96 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 96 LEU VAL PRO GLY SER HIS MET GLY GLY ARG PRO ARG GLN SEQRES 3 A 96 HIS LEU LEU SER LEU THR ARG ARG ALA GLN LYS HIS ARG SEQRES 4 A 96 LEU ARG GLU LEU LYS ILE GLN VAL LYS GLU PHE ALA ASP SEQRES 5 A 96 LYS GLU GLU GLY GLY ASP VAL LYS ALA VAL CYS LEU THR SEQRES 6 A 96 LEU PHE LEU LEU ALA LEU ARG ALA ARG ASN GLU HIS ARG SEQRES 7 A 96 GLN ALA ASP GLU LEU GLU ALA ILE MET GLN GLY ARG GLY SEQRES 8 A 96 SER GLY LEU GLN PRO SEQRES 1 D 14 DA DA DT DT DT DT DC DA DG DA DA DA DC SEQRES 2 D 14 DC SEQRES 1 E 14 DA DG DG DT DT DT DC DT DG DA DA DA DA SEQRES 2 E 14 DC FORMUL 4 HOH *8(H2 O) HELIX 1 1 HIS A 395 LEU A 399 5 5 HELIX 2 2 THR A 400 GLY A 424 1 25 HELIX 3 3 ASP A 426 ALA A 441 1 16 HELIX 4 4 GLU A 444 GLN A 456 1 13 CRYST1 97.470 97.470 69.780 90.00 90.00 90.00 I 4 2 2 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 0.010260 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010260 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014331 0.00000