PDB Short entry for 5KAZ HEADER SIGNALING PROTEIN 02-JUN-16 5KAZ TITLE HUMAN SH2D1B STRUCTURE COMPND MOL_ID: 1; COMPND 2 MOLECULE: SH2 DOMAIN-CONTAINING PROTEIN 1B; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: EWS/FLI1-ACTIVATED TRANSCRIPT 2,EAT-2; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: SH2D1B, EAT2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET11 KEYWDS SH2D1B, EAT2, SLAM, SAP, SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR M.TAHA,E.NEZERWA,H.-J.NAM REVDAT 2 28-FEB-24 5KAZ 1 REMARK REVDAT 1 12-APR-17 5KAZ 0 JRNL AUTH M.TAHA,E.NEZERWA,H.J.NAM JRNL TITL THE X-RAY CRYSTALLOGRAPHIC STRUCTURE OF HUMAN EAT2 (SH2D1B). JRNL REF PROTEIN PEPT. LETT. V. 23 862 2016 JRNL REFN ISSN 1875-5305 JRNL PMID 27586300 REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.8.4_1496 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.19 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.500 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 3 NUMBER OF REFLECTIONS : 13365 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.191 REMARK 3 R VALUE (WORKING SET) : 0.189 REMARK 3 FREE R VALUE : 0.214 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.880 REMARK 3 FREE R VALUE TEST SET COUNT : 652 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 35.1982 - 2.9064 0.97 2620 152 0.1745 0.2083 REMARK 3 2 2.9064 - 2.3070 0.99 2534 139 0.2156 0.2006 REMARK 3 3 2.3070 - 2.0154 0.99 2551 116 0.1917 0.2264 REMARK 3 4 2.0154 - 1.8312 0.99 2498 136 0.1983 0.2417 REMARK 3 5 1.8312 - 1.6999 0.99 2510 109 0.1977 0.2565 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.140 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.350 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.007 866 REMARK 3 ANGLE : 1.209 1166 REMARK 3 CHIRALITY : 0.045 126 REMARK 3 PLANARITY : 0.005 147 REMARK 3 DIHEDRAL : 12.853 336 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5KAZ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 03-JUN-16. REMARK 100 THE DEPOSITION ID IS D_1000221975. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-MAR-06 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.5 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) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 325 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13571 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 31.054 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 200 DATA REDUNDANCY : 4.100 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 33.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL 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: NULL REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.54 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.44 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M NA-CITRATE PH 5.5, 24% PEG 4000, REMARK 280 50 MM (NH)2SO4, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K 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 33.49150 REMARK 290 SMTRY2 9 0.000000 1.000000 0.000000 33.49150 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 52.57750 REMARK 290 SMTRY1 10 -1.000000 0.000000 0.000000 33.49150 REMARK 290 SMTRY2 10 0.000000 -1.000000 0.000000 33.49150 REMARK 290 SMTRY3 10 0.000000 0.000000 1.000000 52.57750 REMARK 290 SMTRY1 11 0.000000 -1.000000 0.000000 33.49150 REMARK 290 SMTRY2 11 1.000000 0.000000 0.000000 33.49150 REMARK 290 SMTRY3 11 0.000000 0.000000 1.000000 52.57750 REMARK 290 SMTRY1 12 0.000000 1.000000 0.000000 33.49150 REMARK 290 SMTRY2 12 -1.000000 0.000000 0.000000 33.49150 REMARK 290 SMTRY3 12 0.000000 0.000000 1.000000 52.57750 REMARK 290 SMTRY1 13 -1.000000 0.000000 0.000000 33.49150 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 33.49150 REMARK 290 SMTRY3 13 0.000000 0.000000 -1.000000 52.57750 REMARK 290 SMTRY1 14 1.000000 0.000000 0.000000 33.49150 REMARK 290 SMTRY2 14 0.000000 -1.000000 0.000000 33.49150 REMARK 290 SMTRY3 14 0.000000 0.000000 -1.000000 52.57750 REMARK 290 SMTRY1 15 0.000000 1.000000 0.000000 33.49150 REMARK 290 SMTRY2 15 1.000000 0.000000 0.000000 33.49150 REMARK 290 SMTRY3 15 0.000000 0.000000 -1.000000 52.57750 REMARK 290 SMTRY1 16 0.000000 -1.000000 0.000000 33.49150 REMARK 290 SMTRY2 16 -1.000000 0.000000 0.000000 33.49150 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 52.57750 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: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 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 406 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 425 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 433 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 444 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 THR A 104 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 HOH A 360 O HOH A 401 1.86 REMARK 500 O HOH A 387 O HOH A 430 2.04 REMARK 500 O HOH A 420 O HOH A 448 2.05 REMARK 500 O HOH A 381 O HOH A 416 2.06 REMARK 500 O HOH A 415 O HOH A 439 2.06 REMARK 500 O HOH A 312 O HOH A 399 2.06 REMARK 500 O HOH A 384 O HOH A 431 2.08 REMARK 500 O HOH A 410 O HOH A 429 2.17 REMARK 500 O HOH A 436 O HOH A 442 2.18 REMARK 500 NH2 ARG A 64 O HOH A 301 2.18 REMARK 500 O GLU A 69 O HOH A 302 2.18 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 LYS A 59 -78.82 -70.22 REMARK 500 HIS A 60 9.46 57.83 REMARK 500 LEU A 98 -69.80 -122.09 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 201 DBREF 5KAZ A 1 104 UNP O14796 SH21B_HUMAN 1 104 SEQRES 1 A 104 MET ASP LEU PRO TYR TYR HIS GLY ARG LEU THR LYS GLN SEQRES 2 A 104 ASP CYS GLU THR LEU LEU LEU LYS GLU GLY VAL ASP GLY SEQRES 3 A 104 ASN PHE LEU LEU ARG ASP SER GLU SER ILE PRO GLY VAL SEQRES 4 A 104 LEU CYS LEU CYS VAL SER PHE LYS ASN ILE VAL TYR THR SEQRES 5 A 104 TYR ARG ILE PHE ARG GLU LYS HIS GLY TYR TYR ARG ILE SEQRES 6 A 104 GLN THR ALA GLU GLY SER PRO LYS GLN VAL PHE PRO SER SEQRES 7 A 104 LEU LYS GLU LEU ILE SER LYS PHE GLU LYS PRO ASN GLN SEQRES 8 A 104 GLY MET VAL VAL HIS LEU LEU LYS PRO ILE LYS ARG THR HET SO4 A 201 5 HETNAM SO4 SULFATE ION FORMUL 2 SO4 O4 S 2- FORMUL 3 HOH *152(H2 O) HELIX 1 AA1 THR A 11 LYS A 21 1 11 HELIX 2 AA2 SER A 78 LYS A 88 1 11 SHEET 1 AA1 6 GLN A 74 PHE A 76 0 SHEET 2 AA1 6 TYR A 63 ILE A 65 -1 N ILE A 65 O GLN A 74 SHEET 3 AA1 6 ILE A 49 ARG A 57 -1 N PHE A 56 O ARG A 64 SHEET 4 AA1 6 LEU A 40 PHE A 46 -1 N LEU A 40 O ILE A 55 SHEET 5 AA1 6 ASN A 27 ASP A 32 -1 N ARG A 31 O CYS A 41 SHEET 6 AA1 6 LYS A 99 PRO A 100 1 O LYS A 99 N PHE A 28 CISPEP 1 GLU A 58 LYS A 59 0 -9.15 SITE 1 AC1 8 LYS A 12 ARG A 31 SER A 33 GLU A 34 SITE 2 AC1 8 CYS A 41 ARG A 54 HOH A 303 HOH A 329 CRYST1 66.983 66.983 105.155 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 0.014929 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014929 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009510 0.00000