PDB Short entry for 5X57 HEADER SIGNALING PROTEIN 15-FEB-17 5X57 TITLE STRUCTURE OF GAR DOMAIN OF ACF7 COMPND MOL_ID: 1; COMPND 2 MOLECULE: MICROTUBULE-ACTIN CROSS-LINKING FACTOR 1, ISOFORMS 1/2/3/5; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 7113-7193; COMPND 5 SYNONYM: SPECTRAPLAKIN PROTEIN, 620 KDA ACTIN-BINDING PROTEIN,ABP620, COMPND 6 ACTIN CROSS-LINKING FAMILY PROTEIN 7,MACROPHIN-1,TRABECULIN-ALPHA; 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: MACF1, ABP620, ACF7, KIAA0465, KIAA1251; SOURCE 6 EXPRESSION_SYSTEM: BACTERIAL ENDOSYMBIONT OF IDAS SP.; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 404293 KEYWDS FUNCTIONAL CLASS, SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR F.YANG,T.WANG,Y.ZHANG,X.Y.WU REVDAT 3 27-MAR-24 5X57 1 REMARK REVDAT 2 06-SEP-17 5X57 1 COMPND SOURCE DBREF REVDAT 1 05-JUL-17 5X57 0 JRNL AUTH Y.MA,J.YUE,Y.ZHANG,C.SHI,M.ODENWALD,W.G.LIANG,Q.WEI,A.GOEL, JRNL AUTH 2 X.GOU,J.ZHANG,S.Y.CHEN,W.J.TANG,J.R.TURNER,F.YANG,H.LIANG, JRNL AUTH 3 H.QIN,X.WU JRNL TITL ACF7 REGULATES INFLAMMATORY COLITIS AND INTESTINAL WOUND JRNL TITL 2 RESPONSE BY ORCHESTRATING TIGHT JUNCTION DYNAMICS. JRNL REF NAT COMMUN V. 8 15375 2017 JRNL REFN ESSN 2041-1723 JRNL PMID 28541346 JRNL DOI 10.1038/NCOMMS15375 REMARK 2 REMARK 2 RESOLUTION. 1.45 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.45 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.84 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 16069 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.130 REMARK 3 R VALUE (WORKING SET) : 0.126 REMARK 3 FREE R VALUE : 0.165 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.010 REMARK 3 FREE R VALUE TEST SET COUNT : 1608 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 28.8436 - 3.2236 0.95 1368 152 0.1631 0.1716 REMARK 3 2 3.2236 - 2.5592 0.99 1336 149 0.1410 0.1782 REMARK 3 3 2.5592 - 2.2358 1.00 1340 148 0.1198 0.1712 REMARK 3 4 2.2358 - 2.0315 1.00 1324 148 0.1163 0.1400 REMARK 3 5 2.0315 - 1.8859 1.00 1321 147 0.1123 0.1527 REMARK 3 6 1.8859 - 1.7747 1.00 1299 144 0.0965 0.1381 REMARK 3 7 1.7747 - 1.6858 1.00 1300 145 0.0969 0.1854 REMARK 3 8 1.6858 - 1.6125 1.00 1297 144 0.1001 0.1517 REMARK 3 9 1.6125 - 1.5504 1.00 1300 145 0.0990 0.1600 REMARK 3 10 1.5504 - 1.4969 1.00 1290 142 0.1013 0.1639 REMARK 3 11 1.4969 - 1.4501 0.98 1286 144 0.1148 0.2000 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) : 0.090 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 14.620 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 : 0.023 695 REMARK 3 ANGLE : 1.780 934 REMARK 3 CHIRALITY : 0.104 98 REMARK 3 PLANARITY : 0.012 126 REMARK 3 DIHEDRAL : 20.138 279 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 5X57 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 21-FEB-17. REMARK 100 THE DEPOSITION ID IS D_1300002946. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-NOV-15 REMARK 200 TEMPERATURE (KELVIN) : 263 REMARK 200 PH : 6.5 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) : 1 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : NONIUS KAPPA CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16069 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.450 REMARK 200 RESOLUTION RANGE LOW (A) : 28.840 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 200 DATA REDUNDANCY : 4.400 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 30.0000 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 (%) : 97.9 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.11400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MIR REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.87 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.32 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: SODIUM CACODYLATE TRIHYDRATE, REMARK 280 (NH4)2SO4, PEG 4000, PH 6.5, EVAPORATION, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 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+1/2,Y+1/2,-Z 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 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 37.02000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 22.99500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 37.02000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 22.99500 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 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 320 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 317 O HOH A 318 2.06 REMARK 500 O HOH A 300 O HOH A 306 2.09 REMARK 500 O HOH A 213 O HOH A 305 2.16 REMARK 500 REMARK 500 REMARK: NULL 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 ASP A 23 CB - CG - OD2 ANGL. DEV. = -7.2 DEGREES REMARK 500 ARG A 33 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 LYS A 39 CD - CE - NZ ANGL. DEV. = 17.0 DEGREES REMARK 500 ARG A 43 NE - CZ - NH1 ANGL. DEV. = -3.5 DEGREES REMARK 500 ARG A 43 NE - CZ - NH2 ANGL. DEV. = 4.0 DEGREES REMARK 500 MET A 73 CG - SD - CE ANGL. DEV. = -12.0 DEGREES REMARK 500 ARG A 94 NE - CZ - NH2 ANGL. DEV. = -3.8 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 THR A 21 -52.28 -132.28 REMARK 500 SER A 70 -1.47 75.79 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 320 DISTANCE = 5.84 ANGSTROMS REMARK 525 HOH A 321 DISTANCE = 6.79 ANGSTROMS REMARK 525 HOH A 322 DISTANCE = 7.31 ANGSTROMS REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NI A 101 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 38 SG REMARK 620 2 CYS A 40 SG 105.1 REMARK 620 3 ASP A 91 OD1 120.0 99.0 REMARK 620 4 CYS A 93 SG 119.4 110.4 101.1 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NI A 101 DBREF 5X57 A 18 98 UNP Q9UPN3 MACF1_HUMAN 7113 7193 SEQRES 1 A 81 TYR ARG PRO THR THR ASP ALA ASP LYS ILE GLU ASP GLU SEQRES 2 A 81 VAL THR ARG GLN VAL ALA GLN CYS LYS CYS ALA LYS ARG SEQRES 3 A 81 PHE GLN VAL GLU GLN ILE GLY GLU ASN LYS TYR ARG PHE SEQRES 4 A 81 GLY ASP SER GLN GLN LEU ARG LEU VAL ARG ILE LEU ARG SEQRES 5 A 81 SER THR VAL MET VAL ARG VAL GLY GLY GLY TRP MET ALA SEQRES 6 A 81 LEU ASP GLU PHE LEU VAL LYS ASN ASP PRO CYS ARG ALA SEQRES 7 A 81 ARG GLY ARG HET NI A 101 1 HETNAM NI NICKEL (II) ION FORMUL 2 NI NI 2+ FORMUL 3 HOH *122(H2 O) HELIX 1 AA1 THR A 22 ALA A 36 1 15 HELIX 2 AA2 LEU A 83 ASP A 91 1 9 HELIX 3 AA3 PRO A 92 ARG A 98 5 7 SHEET 1 AA1 5 VAL A 46 GLN A 48 0 SHEET 2 AA1 5 LYS A 53 PHE A 56 -1 O ARG A 55 N GLU A 47 SHEET 3 AA1 5 LEU A 62 LEU A 68 -1 O ARG A 63 N TYR A 54 SHEET 4 AA1 5 THR A 71 VAL A 76 -1 O ARG A 75 N LEU A 64 SHEET 5 AA1 5 GLY A 79 ALA A 82 -1 O MET A 81 N VAL A 74 LINK SG CYS A 38 NI NI A 101 1555 1555 2.30 LINK SG CYS A 40 NI NI A 101 1555 1555 2.34 LINK OD1 ASP A 91 NI NI A 101 1555 1555 2.04 LINK SG CYS A 93 NI NI A 101 1555 1555 2.34 SITE 1 AC1 4 CYS A 38 CYS A 40 ASP A 91 CYS A 93 CRYST1 74.040 45.990 25.620 90.00 90.00 90.00 P 21 21 2 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 0.013506 0.000000 0.000000 0.00000 SCALE2 0.000000 0.021744 0.000000 0.00000 SCALE3 0.000000 0.000000 0.039032 0.00000