HEADER STRUCTURAL PROTEIN 25-APR-23 8OV0 TITLE MUC5AC CYSD7 AMINO ACIDS 3518-3626 COMPND MOL_ID: 1; COMPND 2 MOLECULE: MUCIN-5AC; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: MUC-5AC,GASTRIC MUCIN,MAJOR AIRWAY GLYCOPROTEIN,MUCIN-5 COMPND 5 SUBTYPE AC,TRACHEOBRONCHIAL,TRACHEOBRONCHIAL MUCIN,TBM; COMPND 6 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: MUC5AC, MUC5; SOURCE 6 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 8 EXPRESSION_SYSTEM_CELL_LINE: HEK 293-F KEYWDS DISULFIDE, MUCUS, CYSD, ASSEMBLY, STRUCTURAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR L.KHMELNITSKY,A.MILO,O.DYM,D.FASS REVDAT 2 15-NOV-23 8OV0 1 JRNL REVDAT 1 16-AUG-23 8OV0 0 JRNL AUTH L.KHMELNITSKY,A.MILO,O.DYM,D.FASS JRNL TITL DIVERSITY OF CYSD DOMAINS IN GEL-FORMING MUCINS. JRNL REF FEBS J. V. 290 5196 2023 JRNL REFN ISSN 1742-464X JRNL PMID 37526947 JRNL DOI 10.1111/FEBS.16918 REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20.1_4487 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 22.00 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.4 REMARK 3 NUMBER OF REFLECTIONS : 10154 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.183 REMARK 3 R VALUE (WORKING SET) : 0.179 REMARK 3 FREE R VALUE : 0.227 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 6.970 REMARK 3 FREE R VALUE TEST SET COUNT : 708 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 22.0000 - 2.9100 0.95 1902 143 0.1671 0.2017 REMARK 3 2 2.9000 - 2.3100 0.96 1864 137 0.1987 0.2890 REMARK 3 3 2.3100 - 2.0200 0.99 1892 139 0.1803 0.2344 REMARK 3 4 2.0200 - 1.8300 0.99 1898 149 0.1829 0.2026 REMARK 3 5 1.8300 - 1.7000 0.99 1890 140 0.1796 0.2336 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 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) : 0.136 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.099 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 12.43 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.99 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 : 0.007 870 REMARK 3 ANGLE : 1.167 1185 REMARK 3 CHIRALITY : 0.071 126 REMARK 3 PLANARITY : 0.009 160 REMARK 3 DIHEDRAL : 6.818 122 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 8OV0 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 25-APR-23. REMARK 100 THE DEPOSITION ID IS D_1292129729. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-MAR-23 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.34050 REMARK 200 MONOCHROMATOR : GA REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : RIGAKU HYPIX-3000 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : CRYSALISPRO REMARK 200 DATA SCALING SOFTWARE : CRYSALISPRO REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10154 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 22.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.3 REMARK 200 DATA REDUNDANCY : 1.800 REMARK 200 R MERGE (I) : 0.02837 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.76 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: PHENIX 1.20.1_4487 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 33.46 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.85 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 150 MM AMMONIUM CHLORIDE 100 MM SODIUM REMARK 280 ACETATE PH 5.1 32% PEG 3350 5% ETHYLENE GLYCOL, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 11.46050 REMARK 290 SMTRY3 2 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: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7000 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 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 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 VAL A 3626 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 ARG A3518 CD NE CZ NH1 NH2 REMARK 470 ARG A3523 CG CD NE CZ NH1 NH2 REMARK 470 ARG A3559 CD NE CZ NH1 NH2 REMARK 470 ARG A3560 CG CD NE CZ NH1 NH2 REMARK 470 GLU A3563 CG CD OE1 OE2 REMARK 470 ARG A3590 CD NE CZ NH1 NH2 REMARK 470 GLU A3591 CD OE1 OE2 REMARK 470 GLN A3602 CD OE1 NE2 REMARK 470 PHE A3605 CG CD1 CD2 CE1 CE2 CZ REMARK 470 LYS A3622 CG CD CE NZ 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 OE2 GLU A 3580 O HOH A 3801 2.08 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 3854 O HOH A 3893 1545 2.11 REMARK 500 O HOH A 3821 O HOH A 3910 1455 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 ILE A3557 -95.96 -104.47 REMARK 500 HIS A3574 56.65 -140.88 REMARK 500 GLU A3592 -38.11 -132.08 REMARK 500 REMARK 500 REMARK: NULL 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 CA A3701 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A3531 OD1 REMARK 620 2 ASP A3533 O 78.1 REMARK 620 3 ASP A3543 OD1 149.6 71.8 REMARK 620 4 ASP A3543 OD2 159.0 121.1 50.9 REMARK 620 5 GLU A3545 OE2 88.5 83.5 84.7 101.6 REMARK 620 6 ASN A3610 OD1 86.4 85.4 94.6 86.7 168.5 REMARK 620 7 TYR A3611 O 80.8 158.9 129.3 79.8 96.1 93.3 REMARK 620 N 1 2 3 4 5 6 DBREF 8OV0 A 3518 3626 UNP P98088 MUC5A_HUMAN 3518 3626 SEQADV 8OV0 GLY A 3516 UNP P98088 EXPRESSION TAG SEQADV 8OV0 GLY A 3517 UNP P98088 EXPRESSION TAG SEQRES 1 A 111 GLY GLY ARG ASP CYS HIS PRO ARG CYS THR TRP THR LYS SEQRES 2 A 111 TRP PHE ASP VAL ASP PHE PRO SER PRO GLY PRO HIS GLY SEQRES 3 A 111 GLY ASP LYS GLU THR TYR ASN ASN ILE ILE ARG SER GLY SEQRES 4 A 111 GLU LYS ILE CYS ARG ARG PRO GLU GLU ILE THR ARG LEU SEQRES 5 A 111 GLN CYS ARG ALA LYS SER HIS PRO GLU VAL SER ILE GLU SEQRES 6 A 111 HIS LEU GLY GLN VAL VAL GLN CYS SER ARG GLU GLU GLY SEQRES 7 A 111 LEU VAL CYS ARG ASN GLN ASP GLN GLN GLY PRO PHE LYS SEQRES 8 A 111 MET CYS LEU ASN TYR GLU VAL ARG VAL LEU CYS CYS GLU SEQRES 9 A 111 THR PRO LYS GLY CYS PRO VAL HET CA A3701 1 HET CL A3702 1 HETNAM CA CALCIUM ION HETNAM CL CHLORIDE ION FORMUL 2 CA CA 2+ FORMUL 3 CL CL 1- FORMUL 4 HOH *121(H2 O) HELIX 1 AA1 TYR A 3547 SER A 3553 1 7 HELIX 2 AA2 SER A 3578 GLY A 3583 5 6 HELIX 3 AA3 GLN A 3599 GLN A 3601 5 3 SHEET 1 AA1 3 ARG A3523 TRP A3526 0 SHEET 2 AA1 3 TYR A3611 GLU A3619 -1 O CYS A3617 N THR A3525 SHEET 3 AA1 3 GLU A3563 ALA A3571 -1 N THR A3565 O LEU A3616 SHEET 1 AA2 3 GLY A3542 THR A3546 0 SHEET 2 AA2 3 GLY A3593 ARG A3597 -1 O LEU A3594 N GLU A3545 SHEET 3 AA2 3 VAL A3586 SER A3589 -1 N SER A3589 O GLY A3593 SSBOND 1 CYS A 3520 CYS A 3624 1555 1555 2.02 SSBOND 2 CYS A 3524 CYS A 3618 1555 1555 2.03 SSBOND 3 CYS A 3558 CYS A 3617 1555 1555 2.02 SSBOND 4 CYS A 3569 CYS A 3588 1555 1555 2.03 SSBOND 5 CYS A 3596 CYS A 3608 1555 1555 2.03 LINK OD1 ASP A3531 CA CA A3701 1555 1555 2.38 LINK O ASP A3533 CA CA A3701 1555 1555 2.36 LINK OD1 ASP A3543 CA CA A3701 1555 1555 2.61 LINK OD2 ASP A3543 CA CA A3701 1555 1555 2.46 LINK OE2 GLU A3545 CA CA A3701 1555 1555 2.29 LINK OD1 ASN A3610 CA CA A3701 1555 1555 2.44 LINK O TYR A3611 CA CA A3701 1555 1555 2.50 CISPEP 1 GLY A 3603 PRO A 3604 0 5.60 CRYST1 30.659 22.921 66.231 90.00 94.91 90.00 P 1 21 1 2 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 0.032617 0.000000 0.002802 0.00000 SCALE2 0.000000 0.043628 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015154 0.00000