PDB Short entry for 5W3R HEADER SIGNALING PROTEIN 08-JUN-17 5W3R TITLE SH2B1 SH2 DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: SH2B ADAPTER PROTEIN 1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: SH2 DOMAIN (UNP RESIDUES 519-628); COMPND 5 SYNONYM: PRO-RICH,PH AND SH2 DOMAIN-CONTAINING SIGNALING MEDIATOR, COMPND 6 PSM,SH2 DOMAIN-CONTAINING PROTEIN 1B; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: SH2B1, KIAA1299, SH2B; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET15B KEYWDS SH2B1, SH2, SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR M.A.MCKERCHER,D.S.WUTTKE REVDAT 4 04-OCT-23 5W3R 1 REMARK REVDAT 3 27-NOV-19 5W3R 1 REMARK REVDAT 2 25-APR-18 5W3R 1 SOURCE JRNL REVDAT 1 22-NOV-17 5W3R 0 JRNL AUTH M.A.MCKERCHER,X.GUAN,Z.TAN,D.S.WUTTKE JRNL TITL DIVERSITY IN PEPTIDE RECOGNITION BY THE SH2 DOMAIN OF SH2B1. JRNL REF PROTEINS V. 86 164 2018 JRNL REFN ESSN 1097-0134 JRNL PMID 29127727 JRNL DOI 10.1002/PROT.25420 REMARK 2 REMARK 2 RESOLUTION. 1.39 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.10.1_2155 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.39 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.37 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 19445 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.146 REMARK 3 R VALUE (WORKING SET) : 0.144 REMARK 3 FREE R VALUE : 0.168 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 972 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 30.3723 - 2.6508 1.00 2806 147 0.1588 0.1700 REMARK 3 2 2.6508 - 2.1042 1.00 2671 141 0.1458 0.1616 REMARK 3 3 2.1042 - 1.8383 1.00 2652 139 0.1255 0.1438 REMARK 3 4 1.8383 - 1.6702 1.00 2627 139 0.1264 0.1779 REMARK 3 5 1.6702 - 1.5505 0.99 2592 136 0.1294 0.1570 REMARK 3 6 1.5505 - 1.4591 0.99 2579 136 0.1293 0.1905 REMARK 3 7 1.4591 - 1.3860 0.98 2546 134 0.1650 0.2245 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.120 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 15.470 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 12.07 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.53 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 : 0.008 956 REMARK 3 ANGLE : 0.975 1290 REMARK 3 CHIRALITY : 0.083 134 REMARK 3 PLANARITY : 0.005 167 REMARK 3 DIHEDRAL : 15.148 335 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 5W3R COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-JUN-17. REMARK 100 THE DEPOSITION ID IS D_1000228307. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-MAR-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.2 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 8.2.2 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 : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA 3.3.22 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19492 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.386 REMARK 200 RESOLUTION RANGE LOW (A) : 52.750 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 6.500 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.08300 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 14.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.39 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.46 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.1 REMARK 200 DATA REDUNDANCY IN SHELL : 5.90 REMARK 200 R MERGE FOR SHELL (I) : 0.32500 REMARK 200 R SYM FOR SHELL (I) : 0.32500 REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 2.6.1 REMARK 200 STARTING MODEL: SOLVED USING A PREVIOUS POOR-RESOLUTION REMARK 200 UNPUBLISHED STRUCTURE, WHICH, IN TURN, WAS SOLVED USING 2HDV AS REMARK 200 A MODEL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 32.95 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.83 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 3350, POTASSIUM SULFATE, PHENOL, REMARK 280 PH 7.2, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 14.50500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 30.36500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 26.37500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 30.36500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 14.50500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 26.37500 REMARK 290 SMTRY3 4 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 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 ASP A 519 CG OD1 OD2 REMARK 470 GLU A 612 CG CD OE1 OE2 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 OE1 GLU A 558 O HOH A 801 2.12 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 861 O HOH A 870 2455 2.07 REMARK 500 NH2 ARG A 560 O GLN A 571 3644 2.10 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 GLN A 571 58.35 29.09 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 PO4 A 701 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IPH A 702 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IPH A 703 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IPH A 704 DBREF 5W3R A 519 628 UNP Q9NRF2 SH2B1_HUMAN 519 628 SEQADV 5W3R GLY A 515 UNP Q9NRF2 EXPRESSION TAG SEQADV 5W3R SER A 516 UNP Q9NRF2 EXPRESSION TAG SEQADV 5W3R HIS A 517 UNP Q9NRF2 EXPRESSION TAG SEQADV 5W3R MET A 518 UNP Q9NRF2 EXPRESSION TAG SEQADV 5W3R ALA A 583 UNP Q9NRF2 GLU 583 ENGINEERED MUTATION SEQADV 5W3R ALA A 584 UNP Q9NRF2 GLU 584 ENGINEERED MUTATION SEQADV 5W3R HIS A 593 UNP Q9NRF2 TRP 593 ENGINEERED MUTATION SEQRES 1 A 114 GLY SER HIS MET ASP GLN PRO LEU SER GLY TYR PRO TRP SEQRES 2 A 114 PHE HIS GLY MET LEU SER ARG LEU LYS ALA ALA GLN LEU SEQRES 3 A 114 VAL LEU THR GLY GLY THR GLY SER HIS GLY VAL PHE LEU SEQRES 4 A 114 VAL ARG GLN SER GLU THR ARG ARG GLY GLU TYR VAL LEU SEQRES 5 A 114 THR PHE ASN PHE GLN GLY LYS ALA LYS HIS LEU ARG LEU SEQRES 6 A 114 SER LEU ASN ALA ALA GLY GLN CYS ARG VAL GLN HIS LEU SEQRES 7 A 114 HIS PHE GLN SER ILE PHE ASP MET LEU GLU HIS PHE ARG SEQRES 8 A 114 VAL HIS PRO ILE PRO LEU GLU SER GLY GLY SER SER ASP SEQRES 9 A 114 VAL VAL LEU VAL SER TYR VAL PRO SER SER HET PO4 A 701 5 HET IPH A 702 13 HET IPH A 703 13 HET IPH A 704 13 HETNAM PO4 PHOSPHATE ION HETNAM IPH PHENOL FORMUL 2 PO4 O4 P 3- FORMUL 3 IPH 3(C6 H6 O) FORMUL 6 HOH *115(H2 O) HELIX 1 AA1 PRO A 521 TYR A 525 5 5 HELIX 2 AA2 SER A 533 THR A 543 1 11 HELIX 3 AA3 GLY A 544 HIS A 549 5 6 HELIX 4 AA4 SER A 596 HIS A 607 1 12 SHEET 1 AA1 6 PHE A 528 MET A 531 0 SHEET 2 AA1 6 VAL A 551 GLN A 556 1 O VAL A 554 N HIS A 529 SHEET 3 AA1 6 TYR A 564 PHE A 570 -1 O VAL A 565 N ARG A 555 SHEET 4 AA1 6 LYS A 573 LEU A 581 -1 O LYS A 573 N PHE A 570 SHEET 5 AA1 6 CYS A 587 VAL A 589 -1 O ARG A 588 N SER A 580 SHEET 6 AA1 6 LEU A 592 PHE A 594 -1 O PHE A 594 N CYS A 587 SHEET 1 AA2 3 PHE A 528 MET A 531 0 SHEET 2 AA2 3 VAL A 551 GLN A 556 1 O VAL A 554 N HIS A 529 SHEET 3 AA2 3 SER A 623 TYR A 624 1 O SER A 623 N PHE A 552 SITE 1 AC1 7 ARG A 534 ARG A 555 SER A 557 GLU A 558 SITE 2 AC1 7 THR A 559 ARG A 578 HOH A 818 SITE 1 AC2 6 GLY A 562 TYR A 564 LEU A 579 LEU A 581 SITE 2 AC2 6 CYS A 587 HOH A 819 SITE 1 AC3 3 ARG A 561 ARG A 605 VAL A 622 SITE 1 AC4 7 PHE A 570 GLN A 590 ILE A 609 PRO A 610 SITE 2 AC4 7 LEU A 611 SER A 617 VAL A 619 CRYST1 29.010 52.750 60.730 90.00 90.00 90.00 P 21 21 21 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 0.034471 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018957 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016466 0.00000