HEADER CELL ADHESION 09-MAR-21 7EB6 TITLE CRYSTAL STRUCTURE OF GTP-BINDING PROTEIN-LIKE DOMAIN OF AGAP1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: ARF-GAP WITH GTPASE, ANK REPEAT AND PH DOMAIN-CONTAINING COMPND 3 PROTEIN 1; COMPND 4 CHAIN: A; COMPND 5 SYNONYM: AGAP-1,CENTAURIN-GAMMA-2,CNT-G2,GTP-BINDING AND GTPASE- COMPND 6 ACTIVATING PROTEIN 1,GGAP1; 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: AGAP1, CENTG2, KIAA1099; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS AGAP1, GTP-BINDING PROTEIN-LIKE DOMAIN, LEUKEMIA, CELL ADHESION EXPDTA X-RAY DIFFRACTION AUTHOR N.CHENG,H.ZHANG,S.ZHANG,X.MA,G.MENG REVDAT 2 29-NOV-23 7EB6 1 REMARK REVDAT 1 21-APR-21 7EB6 0 JRNL AUTH N.CHENG,H.ZHANG,S.ZHANG,X.MA,G.MENG JRNL TITL CRYSTAL STRUCTURE OF THE GTP-BINDING PROTEIN-LIKE DOMAIN OF JRNL TITL 2 AGAP1. JRNL REF ACTA CRYSTALLOGR.,SECT.F V. 77 105 2021 JRNL REFN ESSN 2053-230X JRNL PMID 33830075 JRNL DOI 10.1107/S2053230X21003150 REMARK 2 REMARK 2 RESOLUTION. 3.01 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.14_3260 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) : 3.01 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.49 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 3 NUMBER OF REFLECTIONS : 9136 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.236 REMARK 3 R VALUE (WORKING SET) : 0.233 REMARK 3 FREE R VALUE : 0.265 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.950 REMARK 3 FREE R VALUE TEST SET COUNT : 909 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 35.4930 - 5.4714 0.98 1373 148 0.2098 0.2239 REMARK 3 2 5.4714 - 4.3453 0.99 1376 141 0.1875 0.2105 REMARK 3 3 4.3453 - 3.7967 0.99 1407 159 0.2130 0.2381 REMARK 3 4 3.7967 - 3.4499 0.99 1364 159 0.2613 0.3168 REMARK 3 5 3.4499 - 3.2028 0.99 1371 154 0.2832 0.3201 REMARK 3 6 3.2028 - 3.0141 0.98 1336 148 0.3170 0.3697 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) : 0.460 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 27.070 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 43.32 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: (CHAIN 'A' AND RESID 69 THROUGH 233) REMARK 3 ORIGIN FOR THE GROUP (A): 14.2952 -18.0363 -19.1304 REMARK 3 T TENSOR REMARK 3 T11: 0.1201 T22: 0.0868 REMARK 3 T33: 0.1140 T12: 0.0432 REMARK 3 T13: 0.0488 T23: 0.0920 REMARK 3 L TENSOR REMARK 3 L11: 1.2598 L22: 0.9480 REMARK 3 L33: 0.5759 L12: 0.0485 REMARK 3 L13: -0.2276 L23: -0.4411 REMARK 3 S TENSOR REMARK 3 S11: -0.2152 S12: 0.2597 S13: -0.5017 REMARK 3 S21: 0.4681 S22: -0.0886 S23: -0.2543 REMARK 3 S31: -0.1918 S32: -0.0385 S33: -0.4059 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 7EB6 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 18-MAR-21. REMARK 100 THE DEPOSITION ID IS D_1300020571. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-MAR-20 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 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) : 0.99 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MAR CCD 165 MM REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9136 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.014 REMARK 200 RESOLUTION RANGE LOW (A) : 35.493 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 5.900 REMARK 200 R MERGE (I) : 0.13000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.01 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.12 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 FOR SHELL : NULL 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: 2IWR REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 60.70 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.13 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 8000, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 278K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 4 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+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -Y+1/2,X+1/2,Z+1/2 REMARK 290 8555 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 50.19500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 50.19500 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 24.04000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 50.19500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 50.19500 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 24.04000 REMARK 290 SMTRY1 7 0.000000 -1.000000 0.000000 50.19500 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 50.19500 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 24.04000 REMARK 290 SMTRY1 8 0.000000 1.000000 0.000000 50.19500 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 50.19500 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 24.04000 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 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 64 REMARK 465 SER A 65 REMARK 465 HIS A 66 REMARK 465 MET A 67 REMARK 465 LEU A 68 REMARK 465 LYS A 234 REMARK 465 LYS A 235 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 HH22 ARG A 161 HH TYR A 165 1.33 REMARK 500 SG CYS A 211 OG1 THR A 213 2.00 REMARK 500 O SER A 151 O HOH A 301 2.01 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 GLU A 99 124.76 -21.91 REMARK 500 PRO A 102 1.55 -63.46 REMARK 500 LYS A 109 109.06 -177.95 REMARK 500 PRO A 128 -174.38 -58.43 REMARK 500 LEU A 146 1.20 -67.40 REMARK 500 SER A 183 -172.67 175.75 REMARK 500 ARG A 188 146.65 -39.72 REMARK 500 LYS A 203 44.74 72.75 REMARK 500 ARG A 204 58.15 37.49 REMARK 500 ASN A 217 -0.51 73.21 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 TYR A 214 GLY A 215 149.95 REMARK 500 REMARK 500 REMARK: NULL DBREF 7EB6 A 70 235 UNP Q9UPQ3 AGAP1_HUMAN 70 235 SEQADV 7EB6 GLY A 64 UNP Q9UPQ3 EXPRESSION TAG SEQADV 7EB6 SER A 65 UNP Q9UPQ3 EXPRESSION TAG SEQADV 7EB6 HIS A 66 UNP Q9UPQ3 EXPRESSION TAG SEQADV 7EB6 MET A 67 UNP Q9UPQ3 EXPRESSION TAG SEQADV 7EB6 LEU A 68 UNP Q9UPQ3 EXPRESSION TAG SEQADV 7EB6 GLU A 69 UNP Q9UPQ3 EXPRESSION TAG SEQRES 1 A 172 GLY SER HIS MET LEU GLU PRO GLU LEU LYS VAL GLY ILE SEQRES 2 A 172 VAL GLY ASN LEU ALA SER GLY LYS SER ALA LEU VAL HIS SEQRES 3 A 172 ARG TYR LEU THR GLY THR TYR VAL GLN GLU GLU SER PRO SEQRES 4 A 172 GLU GLY GLY ARG PHE LYS LYS GLU ILE VAL VAL ASP GLY SEQRES 5 A 172 GLN SER TYR LEU LEU LEU ILE ARG ASP GLU GLY GLY PRO SEQRES 6 A 172 PRO GLU ALA GLN PHE ALA MET TRP VAL ASP ALA VAL ILE SEQRES 7 A 172 PHE VAL PHE SER LEU GLU ASP GLU ILE SER PHE GLN THR SEQRES 8 A 172 VAL TYR HIS TYR TYR SER ARG MET ALA ASN TYR ARG ASN SEQRES 9 A 172 THR SER GLU ILE PRO LEU VAL LEU VAL GLY THR GLN ASP SEQRES 10 A 172 ALA ILE SER SER ALA ASN PRO ARG VAL ILE ASP ASP ALA SEQRES 11 A 172 ARG ALA ARG LYS LEU SER ASN ASP LEU LYS ARG CYS THR SEQRES 12 A 172 TYR TYR GLU THR CYS ALA THR TYR GLY LEU ASN VAL GLU SEQRES 13 A 172 ARG VAL PHE GLN ASP VAL ALA GLN LYS ILE VAL ALA THR SEQRES 14 A 172 ARG LYS LYS FORMUL 2 HOH *4(H2 O) HELIX 1 AA1 GLY A 83 GLY A 94 1 12 HELIX 2 AA2 GLU A 130 VAL A 137 1 8 HELIX 3 AA3 ASP A 148 ASN A 164 1 17 HELIX 4 AA4 ASP A 191 LEU A 202 1 12 HELIX 5 AA5 ASN A 217 THR A 232 1 16 SHEET 1 AA1 6 GLY A 105 VAL A 113 0 SHEET 2 AA1 6 GLN A 116 ASP A 124 -1 O TYR A 118 N ILE A 111 SHEET 3 AA1 6 GLU A 71 VAL A 77 1 N LEU A 72 O LEU A 121 SHEET 4 AA1 6 ALA A 139 SER A 145 1 O VAL A 143 N VAL A 77 SHEET 5 AA1 6 LEU A 173 THR A 178 1 O VAL A 174 N PHE A 142 SHEET 6 AA1 6 THR A 206 THR A 210 1 O TYR A 208 N GLY A 177 CRYST1 100.390 100.390 48.080 90.00 90.00 90.00 I 4 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 0.009961 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009961 0.000000 0.00000 SCALE3 0.000000 0.000000 0.020799 0.00000