HEADER SIGNALING PROTEIN 26-OCT-15 5EFX TITLE CRYSTAL STRUCTURE OF RHO GTPASE REGULATOR COMPND MOL_ID: 1; COMPND 2 MOLECULE: RHO GUANINE NUCLEOTIDE EXCHANGE FACTOR 2; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 439-582; COMPND 5 SYNONYM: GUANINE NUCLEOTIDE EXCHANGE FACTOR H1,GEF-H1,MICROTUBULE- COMPND 6 REGULATED RHO-GEF,PROLIFERATING CELL NUCLEOLAR ANTIGEN P40; COMPND 7 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: ARHGEF2, KIAA0651, LFP40; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI 'BL21-GOLD(DE3)PLYSS AG'; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 866768 KEYWDS RHO GTPASE, ACTIVITY, SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR Y.JIANG,S.OUYANG,Z.J.LIU REVDAT 2 08-NOV-23 5EFX 1 JRNL REMARK REVDAT 1 29-JUN-16 5EFX 0 JRNL AUTH Y.JIANG,H.JIANG,S.ZHOU,B.MENG,Z.J.LIU,S.OUYANG JRNL TITL CRYSTAL STRUCTURE OF HGEF-H1 PH DOMAIN PROVIDES INSIGHT INTO JRNL TITL 2 INCAPABILITY IN PHOSPHOINOSITIDE BINDING JRNL REF BIOCHEM.BIOPHYS.RES.COMMUN. V. 471 621 2016 JRNL REFN ESSN 1090-2104 JRNL PMID 26820534 JRNL DOI 10.1016/J.BBRC.2016.01.150 REMARK 2 REMARK 2 RESOLUTION. 2.45 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8.1_1168) 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) : 2.45 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.18 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.0 REMARK 3 NUMBER OF REFLECTIONS : 7003 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.219 REMARK 3 R VALUE (WORKING SET) : 0.217 REMARK 3 FREE R VALUE : 0.253 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.710 REMARK 3 FREE R VALUE TEST SET COUNT : 330 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 36.1812 - 3.0872 1.00 3508 150 0.2035 0.2315 REMARK 3 2 3.0872 - 2.4505 0.94 3165 180 0.2661 0.3079 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) : 0.310 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 27.090 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 47.70 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 40.00 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 : 0.009 1189 REMARK 3 ANGLE : 1.213 1609 REMARK 3 CHIRALITY : 0.078 181 REMARK 3 PLANARITY : 0.005 208 REMARK 3 DIHEDRAL : 15.030 463 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 5EFX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 27-OCT-15. REMARK 100 THE DEPOSITION ID IS D_1000214767. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-JUL-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.8 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL17U REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.98 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 : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 7006 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.450 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.2 REMARK 200 DATA REDUNDANCY : 12.50 REMARK 200 R MERGE (I) : 0.06800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 60.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.45 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.51 REMARK 200 COMPLETENESS FOR SHELL (%) : 77.2 REMARK 200 DATA REDUNDANCY IN SHELL : 10.60 REMARK 200 R MERGE FOR SHELL (I) : 0.36100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 8.290 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: 4D0N REMARK 200 REMARK 200 REMARK: CUBIC CRYSTALS, VERY BEAUTIFUL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.07 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.74 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M SODIUM NITRATE, 20% PEG 3350, PH REMARK 280 6.8, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 289.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 2 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 -X,Y,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+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 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 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 18.97400 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 40.91250 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 59.91500 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 18.97400 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 40.91250 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 59.91500 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 18.97400 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 40.91250 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 59.91500 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 18.97400 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 40.91250 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 59.91500 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 630 LIES ON A SPECIAL POSITION. 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 622 O HOH A 629 1.93 REMARK 500 NH2 ARG A 559 O HOH A 601 1.94 REMARK 500 OD1 ASP A 530 NH1 ARG A 559 2.01 REMARK 500 O PRO A 456 O HOH A 602 2.04 REMARK 500 O GLN A 524 O HOH A 603 2.06 REMARK 500 O HOH A 610 O HOH A 627 2.18 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 620 O HOH A 623 2455 1.86 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 508 1.15 58.92 REMARK 500 GLN A 534 77.46 -118.63 REMARK 500 GLU A 535 -19.81 -44.40 REMARK 500 REMARK 500 REMARK: NULL DBREF 5EFX A 439 582 UNP Q92974 ARHG2_HUMAN 439 582 SEQRES 1 A 144 GLY ALA ARG LEU GLN GLU ILE TYR ASN ARG MET ASP PRO SEQRES 2 A 144 ARG ALA GLN THR PRO VAL PRO GLY LYS GLY PRO PHE GLY SEQRES 3 A 144 ARG GLU GLU LEU LEU ARG ARG LYS LEU ILE HIS ASP GLY SEQRES 4 A 144 CYS LEU LEU TRP LYS THR ALA THR GLY ARG PHE LYS ASP SEQRES 5 A 144 VAL LEU VAL LEU LEU MET THR ASP VAL LEU VAL PHE LEU SEQRES 6 A 144 GLN GLU LYS ASP GLN LYS TYR ILE PHE PRO THR LEU ASP SEQRES 7 A 144 LYS PRO SER VAL VAL SER LEU GLN ASN LEU ILE VAL ARG SEQRES 8 A 144 ASP ILE ALA ASN GLN GLU LYS GLY MET PHE LEU ILE SER SEQRES 9 A 144 ALA ALA PRO PRO GLU MET TYR GLU VAL HIS THR ALA SER SEQRES 10 A 144 ARG ASP ASP ARG SER THR TRP ILE ARG VAL ILE GLN GLN SEQRES 11 A 144 SER VAL ARG THR CYS PRO SER ARG GLU ASP PHE PRO LEU SEQRES 12 A 144 ILE FORMUL 2 HOH *30(H2 O) HELIX 1 AA1 GLY A 439 ARG A 448 1 10 HELIX 2 AA2 ARG A 465 ARG A 470 1 6 HELIX 3 AA3 SER A 555 THR A 572 1 18 SHEET 1 AA1 2 GLN A 454 VAL A 457 0 SHEET 2 AA1 2 GLY A 461 GLY A 464 -1 N GLY A 461 O VAL A 457 SHEET 1 AA2 7 VAL A 520 SER A 522 0 SHEET 2 AA2 7 VAL A 499 LEU A 503 -1 N LEU A 500 O VAL A 521 SHEET 3 AA2 7 PHE A 488 MET A 496 -1 N MET A 496 O VAL A 499 SHEET 4 AA2 7 LEU A 473 LYS A 482 -1 N HIS A 475 O LEU A 495 SHEET 5 AA2 7 GLU A 547 HIS A 552 -1 O GLU A 550 N LYS A 482 SHEET 6 AA2 7 GLY A 537 SER A 542 -1 N LEU A 540 O TYR A 549 SHEET 7 AA2 7 ILE A 527 ASP A 530 -1 N ARG A 529 O PHE A 539 CISPEP 1 ALA A 544 PRO A 545 0 -16.65 CRYST1 37.948 81.825 119.830 90.00 90.00 90.00 I 2 2 2 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 0.026352 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012221 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008345 0.00000