HEADER CYTOKINE 13-MAR-21 7ECQ TITLE CRYSTAL STRUCTURE OF FAM3A COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN FAM3A; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 GENE: FAM3A; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS REGULATOR, CYTOKINE EXPDTA X-RAY DIFFRACTION AUTHOR Z.CHANG,C.SHI REVDAT 2 29-NOV-23 7ECQ 1 REMARK REVDAT 1 27-APR-22 7ECQ 0 JRNL AUTH Z.CHANG,C.SHI JRNL TITL HIGH RESOLUTION CRYSTAL STRUCTURE OF FAM3A SHED LIGHTS ON JRNL TITL 2 ITS FUNCTION ON BETA-OXIDATION JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.38 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.13_2998 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) : 1.38 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.45 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.370 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.3 REMARK 3 NUMBER OF REFLECTIONS : 39699 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.164 REMARK 3 R VALUE (WORKING SET) : 0.163 REMARK 3 FREE R VALUE : 0.171 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.960 REMARK 3 FREE R VALUE TEST SET COUNT : 1971 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 3.3289 - 2.6424 1.00 2803 144 0.1676 0.1789 REMARK 3 2 2.6424 - 2.3084 1.00 2764 150 0.1707 0.1761 REMARK 3 3 2.3084 - 2.0974 0.99 2715 134 0.1400 0.1436 REMARK 3 4 2.0974 - 1.9471 0.99 2723 142 0.1565 0.1833 REMARK 3 5 1.9471 - 1.8323 0.99 2723 121 0.1547 0.1752 REMARK 3 6 1.8323 - 1.7405 0.99 2694 142 0.1682 0.1893 REMARK 3 7 1.7405 - 1.6647 0.98 2659 144 0.1655 0.1948 REMARK 3 8 1.6647 - 1.6007 0.99 2662 133 0.1592 0.1902 REMARK 3 9 1.6007 - 1.5454 0.98 2653 130 0.1648 0.1888 REMARK 3 10 1.5454 - 1.4971 0.98 2679 133 0.1564 0.1659 REMARK 3 11 1.4971 - 1.4543 0.98 2605 142 0.1600 0.1620 REMARK 3 12 1.4543 - 1.4160 0.97 2649 148 0.1711 0.1873 REMARK 3 13 1.4300 - 1.3900 0.99 2900 168 0.1500 0.1542 REMARK 3 14 1.4160 - 1.3815 0.94 2499 140 0.1878 0.2080 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) : 0.110 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 15.650 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 12.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 17.69 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 : 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 7ECQ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 16-MAR-21. REMARK 100 THE DEPOSITION ID IS D_1300021163. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-JUN-14 REMARK 200 TEMPERATURE (KELVIN) : 93 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : BL-5A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.968 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : ADXV REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 39780 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.380 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 (%) : 95.4 REMARK 200 DATA REDUNDANCY : 14.40 REMARK 200 R MERGE (I) : 0.05500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 44.3500 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.38 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.43 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.39400 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: MOLREP REMARK 200 STARTING MODEL: 2YOQ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.26 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.47 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M AMMONIUM SULFATE, 0.1 M MES REMARK 280 PH6.5, 30% W/V POLYETHYLENE GLYCOL MONOMETHYL ETHER 5000, REMARK 280 EVAPORATION, TEMPERATURE 289.15K 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 20.09300 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 39.45350 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 30.39100 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 39.45350 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 20.09300 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 30.39100 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 TOTAL BURIED SURFACE AREA: 160 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9080 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -12.0 KCAL/MOL 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 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 446 O HOH A 607 1.97 REMARK 500 OE1 GLU A 142 O HOH A 401 1.99 REMARK 500 O HOH A 534 O HOH A 620 2.05 REMARK 500 OE2 GLU A 67 O HOH A 402 2.08 REMARK 500 OE1 GLU A 211 O HOH A 403 2.11 REMARK 500 O HOH A 624 O HOH A 629 2.14 REMARK 500 O HOH A 433 O HOH A 627 2.17 REMARK 500 NE ARG A 138 O HOH A 404 2.19 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 604 O HOH A 627 3555 1.97 REMARK 500 O HOH A 606 O HOH A 614 4545 1.99 REMARK 500 O HOH A 587 O HOH A 633 2455 2.00 REMARK 500 O HOH A 595 O HOH A 648 3545 2.09 REMARK 500 O HOH A 552 O HOH A 614 4545 2.17 REMARK 500 O HOH A 426 O HOH A 530 1655 2.19 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 TYR A 57 -163.09 -109.07 REMARK 500 ALA A 79 -133.06 50.82 REMARK 500 PRO A 139 50.66 -92.27 REMARK 500 ASP A 152 -76.75 74.85 REMARK 500 PHE A 179 121.74 -37.72 REMARK 500 GLN A 192 -69.47 -96.83 REMARK 500 REMARK 500 REMARK: NULL DBREF 7ECQ A 56 230 UNP Q9D8T0 FAM3A_MOUSE 56 230 SEQRES 1 A 175 LYS TYR LYS CYS GLY LEU PRO GLN PRO CYS PRO GLU GLU SEQRES 2 A 175 HIS LEU SER PHE ARG ILE VAL SER GLY ALA ALA ASN VAL SEQRES 3 A 175 ILE GLY PRO LYS ILE CYS LEU GLU ASP LYS MET LEU MET SEQRES 4 A 175 SER SER VAL LYS ASP ASN VAL GLY ARG GLY LEU ASN ILE SEQRES 5 A 175 ALA LEU VAL ASN GLY VAL SER GLY GLU LEU LEU GLU ALA SEQRES 6 A 175 ARG ALA PHE ASP MET TRP ALA GLY ASP VAL ASN ASP LEU SEQRES 7 A 175 LEU LYS PHE ILE ARG PRO LEU HIS GLU GLY THR LEU VAL SEQRES 8 A 175 PHE VAL ALA SER TYR ASP ASP PRO ALA THR LYS MET ASN SEQRES 9 A 175 GLU GLU THR ARG LYS LEU PHE SER GLU LEU GLY SER ARG SEQRES 10 A 175 ASN ALA LYS ASP LEU ALA PHE ARG ASP SER TRP VAL PHE SEQRES 11 A 175 VAL GLY ALA LYS GLY VAL GLN ASN LYS SER PRO PHE GLU SEQRES 12 A 175 GLN HIS MET LYS ASN SER LYS HIS THR ASN LYS TYR GLU SEQRES 13 A 175 GLY TRP PRO GLU ALA LEU GLU MET GLU GLY CYS ILE PRO SEQRES 14 A 175 ARG ARG SER ILE ALA GLY HET J0R A 301 11 HET SO4 A 302 5 HETNAM J0R [(2R)-1-(TRIMETHYL-$L^4-AZANYL)PROPAN-2-YL] ETHANOATE HETNAM SO4 SULFATE ION FORMUL 2 J0R C8 H18 N O2 1+ FORMUL 3 SO4 O4 S 2- FORMUL 4 HOH *257(H2 O) HELIX 1 AA1 TYR A 57 LEU A 61 5 5 HELIX 2 AA2 ASP A 129 ARG A 138 1 10 HELIX 3 AA3 ASN A 159 LEU A 169 1 11 HELIX 4 AA4 ASN A 173 LEU A 177 5 5 SHEET 1 AA1 4 LYS A 91 MET A 94 0 SHEET 2 AA1 4 LYS A 85 LEU A 88 -1 N LEU A 88 O LYS A 91 SHEET 3 AA1 4 LEU A 70 VAL A 75 -1 N ARG A 73 O CYS A 87 SHEET 4 AA1 4 GLU A 218 ILE A 223 -1 O ILE A 223 N LEU A 70 SHEET 1 AA2 5 LEU A 117 PHE A 123 0 SHEET 2 AA2 5 GLY A 104 VAL A 110 -1 N LEU A 109 O GLU A 119 SHEET 3 AA2 5 LEU A 145 TYR A 151 -1 O TYR A 151 N GLY A 104 SHEET 4 AA2 5 SER A 182 ALA A 188 -1 O PHE A 185 N VAL A 148 SHEET 5 AA2 5 GLU A 198 MET A 201 -1 O MET A 201 N SER A 182 SSBOND 1 CYS A 59 CYS A 87 1555 1555 2.10 SSBOND 2 CYS A 65 CYS A 222 1555 1555 2.02 CRYST1 40.186 60.782 78.907 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 0.024884 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016452 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012673 0.00000