HEADER ALLERGEN 15-APR-15 4ZCE TITLE CRYSTAL STRUCTURE OF THE DUST MITE ALLERGEN DER P 23 FROM TITLE 2 DERMATOPHAGOIDES PTERONYSSINUS COMPND MOL_ID: 1; COMPND 2 MOLECULE: DUST MITE ALLERGEN; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: UNP RESIDUES 44-90; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DERMATOPHAGOIDES PTERONYSSINUS; SOURCE 3 ORGANISM_COMMON: EUROPEAN HOUSE DUST MITE; SOURCE 4 ORGANISM_TAXID: 6956; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: ROSETTA2; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PDEST KEYWDS DUST, MITE, ALLERGEN, DER P 23 EXPDTA X-RAY DIFFRACTION AUTHOR L.C.PEDERSEN,G.A.MUELLER,T.A.RANDALL,J.GLESNER,L.PERERA,L.L.EDWARDS, AUTHOR 2 M.D.CHAPMAN,R.E.LONDON,A.POMES REVDAT 5 11-DEC-19 4ZCE 1 REMARK REVDAT 4 20-SEP-17 4ZCE 1 REMARK REVDAT 3 10-FEB-16 4ZCE 1 JRNL REVDAT 2 09-DEC-15 4ZCE 1 JRNL REVDAT 1 25-NOV-15 4ZCE 0 JRNL AUTH G.A.MUELLER,T.A.RANDALL,J.GLESNER,L.C.PEDERSEN,L.PERERA, JRNL AUTH 2 L.L.EDWARDS,E.F.DEROSE,M.D.CHAPMAN,R.E.LONDON,A.POMES JRNL TITL SEROLOGICAL, GENOMIC AND STRUCTURAL ANALYSES OF THE MAJOR JRNL TITL 2 MITE ALLERGEN DER P 23. JRNL REF CLIN EXP ALLERGY V. 46 365 2016 JRNL REFN ESSN 1365-2222 JRNL PMID 26602749 JRNL DOI 10.1111/CEA.12680 REMARK 2 REMARK 2 RESOLUTION. 1.55 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.8.2_1309 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) : 1.55 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 26.76 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.9 REMARK 3 NUMBER OF REFLECTIONS : 15142 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.165 REMARK 3 R VALUE (WORKING SET) : 0.164 REMARK 3 FREE R VALUE : 0.190 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.720 REMARK 3 FREE R VALUE TEST SET COUNT : 714 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 26.7635 - 2.6505 1.00 3014 162 0.1581 0.1831 REMARK 3 2 2.6505 - 2.1040 1.00 2953 155 0.1641 0.1788 REMARK 3 3 2.1040 - 1.8381 1.00 2964 142 0.1571 0.1863 REMARK 3 4 1.8381 - 1.6701 0.95 2840 124 0.1827 0.2186 REMARK 3 5 1.6701 - 1.5500 0.90 2657 131 0.1813 0.2481 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) : 0.100 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.490 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 : 0.012 859 REMARK 3 ANGLE : 1.219 1169 REMARK 3 CHIRALITY : 0.079 108 REMARK 3 PLANARITY : 0.008 161 REMARK 3 DIHEDRAL : 12.069 304 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 4ZCE COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 17-APR-15. REMARK 100 THE DEPOSITION ID IS D_1000209032. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-APR-14 REMARK 200 TEMPERATURE (KELVIN) : 173 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : NULL 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 MICROMAX-007 HF REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.514 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : SAD REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RIGAKU SATURN 944+ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15162 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.550 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 (%) : 96.9 REMARK 200 DATA REDUNDANCY : 9.500 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.05800 REMARK 200 FOR THE DATA SET : 18.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.55 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.58 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) : 0.22500 REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: HKL-3000 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.26 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.29 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 50% PBS BUFFER FOR TWO MONTHS IN, PH REMARK 280 7.5, SMALL TUBES, TEMPERATURE 277K 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 26.75950 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 300 REMARK: AS PER THE AUTHORS THE BIOLOGICAL ASSEMBLY IS UNKNOWN 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1010 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6550 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -2.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 SER A 41 REMARK 465 PHE A 42 REMARK 465 SER B 41 REMARK 465 PHE B 42 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 LYS A 44 CD CE NZ REMARK 470 LYS A 58 CE NZ REMARK 470 GLU A 70 CG CD OE1 OE2 REMARK 470 LYS B 44 CE NZ REMARK 470 LYS B 58 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 O HOH A 213 O HOH A 289 1.88 REMARK 500 O HOH B 175 O HOH B 197 1.94 REMARK 500 O HOH B 170 O HOH B 196 2.03 REMARK 500 O HOH A 231 O HOH B 118 2.10 REMARK 500 O HOH A 207 O HOH A 250 2.11 REMARK 500 O HOH A 207 O HOH A 252 2.13 REMARK 500 OD1 ASP B 85 O HOH B 101 2.15 REMARK 500 OE2 GLU A 87 O HOH A 201 2.15 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 ASP B 59 112.73 -161.57 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 296 DISTANCE = 6.11 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 101 DBREF 4ZCE A 44 90 UNP L7N6F8 L7N6F8_DERPT 44 90 DBREF 4ZCE B 44 90 UNP L7N6F8 L7N6F8_DERPT 44 90 SEQADV 4ZCE SER A 41 UNP L7N6F8 EXPRESSION TAG SEQADV 4ZCE PHE A 42 UNP L7N6F8 EXPRESSION TAG SEQADV 4ZCE THR A 43 UNP L7N6F8 EXPRESSION TAG SEQADV 4ZCE SER B 41 UNP L7N6F8 EXPRESSION TAG SEQADV 4ZCE PHE B 42 UNP L7N6F8 EXPRESSION TAG SEQADV 4ZCE THR B 43 UNP L7N6F8 EXPRESSION TAG SEQRES 1 A 50 SER PHE THR LYS PHE GLU CYS PRO SER ARG PHE GLY TYR SEQRES 2 A 50 PHE ALA ASP PRO LYS ASP PRO HIS LYS PHE TYR ILE CYS SEQRES 3 A 50 SER ASN TRP GLU ALA VAL HIS LYS ASP CYS PRO GLY ASN SEQRES 4 A 50 THR ARG TRP ASN GLU ASP GLU GLU THR CYS THR SEQRES 1 B 50 SER PHE THR LYS PHE GLU CYS PRO SER ARG PHE GLY TYR SEQRES 2 B 50 PHE ALA ASP PRO LYS ASP PRO HIS LYS PHE TYR ILE CYS SEQRES 3 B 50 SER ASN TRP GLU ALA VAL HIS LYS ASP CYS PRO GLY ASN SEQRES 4 B 50 THR ARG TRP ASN GLU ASP GLU GLU THR CYS THR HET EDO A 101 10 HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 3 EDO C2 H6 O2 FORMUL 4 HOH *200(H2 O) SHEET 1 AA1 3 GLY A 52 ALA A 55 0 SHEET 2 AA1 3 LYS A 62 SER A 67 -1 O CYS A 66 N GLY A 52 SHEET 3 AA1 3 GLU A 70 ASP A 75 -1 O LYS A 74 N PHE A 63 SHEET 1 AA2 2 ARG A 81 ASN A 83 0 SHEET 2 AA2 2 THR A 88 THR A 90 -1 O THR A 88 N ASN A 83 SHEET 1 AA3 3 GLY B 52 ALA B 55 0 SHEET 2 AA3 3 LYS B 62 SER B 67 -1 O CYS B 66 N GLY B 52 SHEET 3 AA3 3 GLU B 70 ASP B 75 -1 O LYS B 74 N PHE B 63 SHEET 1 AA4 2 TRP B 82 ASN B 83 0 SHEET 2 AA4 2 THR B 88 CYS B 89 -1 O THR B 88 N ASN B 83 SSBOND 1 CYS A 47 CYS A 66 1555 1555 2.06 SSBOND 2 CYS A 76 CYS A 89 1555 1555 2.07 SSBOND 3 CYS B 47 CYS B 66 1555 1555 2.08 SSBOND 4 CYS B 76 CYS B 89 1555 1555 2.08 SITE 1 AC1 5 LYS A 62 HIS A 73 ASP A 75 HOH A 225 SITE 2 AC1 5 HOH A 275 CRYST1 25.283 53.519 40.395 90.00 95.47 90.00 P 1 21 1 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 0.039552 0.000000 0.003788 0.00000 SCALE2 0.000000 0.018685 0.000000 0.00000 SCALE3 0.000000 0.000000 0.024869 0.00000