HEADER HYDROLASE 05-MAY-17 5VPK TITLE CRYSTAL STRUCTURE OF MITE ALLERGEN DER F 1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: DER F 1 VARIANT; COMPND 3 CHAIN: A, B, C; COMPND 4 FRAGMENT: SEQUENCE DATABASE RESIDUES 99-321 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DERMATOPHAGOIDES FARINAE; SOURCE 3 ORGANISM_COMMON: AMERICAN HOUSE DUST MITE; SOURCE 4 ORGANISM_TAXID: 6954 KEYWDS ALLERGY, DUST MITES, ALLERGEN, GLYCOPROTEIN, HYDROLASE, PROTEASE, KEYWDS 2 SECRETED, THIOL PROTEASE, ZYMOGEN EXPDTA X-RAY DIFFRACTION AUTHOR M.CHRUSZCZ,M.D.CHAPMAN,L.D.VAILES,A.POMES,W.MINOR REVDAT 4 04-OCT-23 5VPK 1 REMARK REVDAT 3 13-APR-22 5VPK 1 AUTHOR JRNL HETSYN REVDAT 2 29-JUL-20 5VPK 1 COMPND REMARK HETNAM LINK REVDAT 2 2 1 SITE REVDAT 1 24-MAY-17 5VPK 0 SPRSDE 24-MAY-17 5VPK 3D6S JRNL AUTH M.CHRUSZCZ,M.D.CHAPMAN,L.D.VAILES,E.A.STURA,J.M.SAINT-REMY, JRNL AUTH 2 W.MINOR,A.POMES JRNL TITL CRYSTAL STRUCTURES OF MITE ALLERGENS DER F 1 AND DER P 1 JRNL TITL 2 REVEAL DIFFERENCES IN SURFACE-EXPOSED RESIDUES THAT MAY JRNL TITL 3 INFLUENCE ANTIBODY BINDING JRNL REF J.MOL.BIOL. V. 386 520 2009 JRNL REFN ISSN 0022-2836 JRNL PMID 19136006 JRNL DOI 10.1016/J.JMB.2008.12.049 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0158 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.10 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 92.4 REMARK 3 NUMBER OF REFLECTIONS : 37834 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.181 REMARK 3 R VALUE (WORKING SET) : 0.180 REMARK 3 FREE R VALUE : 0.210 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 1958 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.05 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2978 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.2060 REMARK 3 BIN FREE R VALUE SET COUNT : 167 REMARK 3 BIN FREE R VALUE : 0.2740 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5238 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 58 REMARK 3 SOLVENT ATOMS : 289 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 40.66 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -15.61000 REMARK 3 B22 (A**2) : -15.61000 REMARK 3 B33 (A**2) : 31.22000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.048 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.036 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): NULL REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.959 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.949 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5463 ; 0.012 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 4629 ; 0.000 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7463 ; 1.421 ; 1.931 REMARK 3 BOND ANGLES OTHERS (DEGREES): 10730 ; 3.872 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 672 ; 5.349 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 274 ;33.791 ;23.869 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 807 ;14.297 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 37 ;15.706 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 799 ; 0.086 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 6227 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1160 ; 0.009 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 2687 ; 0.900 ; 1.640 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 2687 ; 0.900 ; 1.640 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3359 ; 1.442 ; 2.453 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 3360 ; 1.442 ; 2.453 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2776 ; 1.189 ; 1.846 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 2761 ; 1.114 ; 1.811 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 4081 ; 1.803 ; 2.671 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 6168 ; 5.590 ;19.877 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 6169 ; 5.590 ;19.881 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NCS TYPE: LOCAL REMARK 3 NUMBER OF DIFFERENT NCS PAIRS : 3 REMARK 3 GROUP CHAIN1 RANGE CHAIN2 RANGE COUNT RMS WEIGHT REMARK 3 1 A 1 223 B 1 223 14538 0.09 0.05 REMARK 3 2 A 1 223 C 1 223 14056 0.08 0.05 REMARK 3 3 B 1 223 C 1 223 13978 0.09 0.05 REMARK 3 REMARK 3 TWIN DETAILS REMARK 3 NUMBER OF TWIN DOMAINS : 2 REMARK 3 TWIN DOMAIN : 1 REMARK 3 TWIN OPERATOR : H, K, L REMARK 3 TWIN FRACTION : 0.597 REMARK 3 TWIN DOMAIN : 2 REMARK 3 TWIN OPERATOR : -H, K, -L REMARK 3 TWIN FRACTION : 0.403 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 3 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 1 A 223 REMARK 3 ORIGIN FOR THE GROUP (A): -23.1970 1.3860 6.8190 REMARK 3 T TENSOR REMARK 3 T11: 0.2561 T22: 0.1978 REMARK 3 T33: 0.0171 T12: 0.0325 REMARK 3 T13: 0.0410 T23: 0.0267 REMARK 3 L TENSOR REMARK 3 L11: 1.2877 L22: 2.1557 REMARK 3 L33: 1.3490 L12: -0.2904 REMARK 3 L13: 0.2703 L23: 0.0222 REMARK 3 S TENSOR REMARK 3 S11: -0.0055 S12: -0.0658 S13: -0.0668 REMARK 3 S21: -0.0775 S22: 0.0784 S23: 0.0991 REMARK 3 S31: -0.1284 S32: 0.0052 S33: -0.0730 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 1 B 223 REMARK 3 ORIGIN FOR THE GROUP (A): -44.2630 22.4400 -6.5320 REMARK 3 T TENSOR REMARK 3 T11: 0.2029 T22: 0.3208 REMARK 3 T33: 0.0154 T12: 0.0206 REMARK 3 T13: -0.0125 T23: 0.0047 REMARK 3 L TENSOR REMARK 3 L11: 3.0374 L22: 1.3561 REMARK 3 L33: 1.2241 L12: -0.0204 REMARK 3 L13: 0.1504 L23: 0.0049 REMARK 3 S TENSOR REMARK 3 S11: 0.0149 S12: -0.4093 S13: -0.1658 REMARK 3 S21: -0.0156 S22: 0.0454 S23: 0.0579 REMARK 3 S31: -0.0190 S32: 0.0127 S33: -0.0602 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : C 1 C 223 REMARK 3 ORIGIN FOR THE GROUP (A): -61.7940 -14.8450 0.0470 REMARK 3 T TENSOR REMARK 3 T11: 0.2600 T22: 0.4499 REMARK 3 T33: 0.0444 T12: 0.0068 REMARK 3 T13: -0.0209 T23: 0.1001 REMARK 3 L TENSOR REMARK 3 L11: 3.6767 L22: 2.0239 REMARK 3 L33: 3.6430 L12: 1.1214 REMARK 3 L13: -1.3934 L23: -2.0188 REMARK 3 S TENSOR REMARK 3 S11: -0.0861 S12: 0.6741 S13: 0.3328 REMARK 3 S21: -0.0813 S22: 0.3839 S23: 0.2235 REMARK 3 S31: -0.0513 S32: -0.4039 S33: -0.2977 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 5VPK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 08-MAY-17. REMARK 100 THE DEPOSITION ID IS D_1000227814. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-FEB-08 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 10.50 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 19-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9794 REMARK 200 MONOCHROMATOR : SI 111 CHANNEL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 40623 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.1 REMARK 200 DATA REDUNDANCY : 6.500 REMARK 200 R MERGE (I) : 0.08800 REMARK 200 R SYM (I) : 0.08800 REMARK 200 FOR THE DATA SET : 34.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.03 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 6.70 REMARK 200 R MERGE FOR SHELL (I) : 0.59100 REMARK 200 R SYM FOR SHELL (I) : 0.59100 REMARK 200 FOR SHELL : 4.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: HKL-3000, MOLREP, PHASER REMARK 200 STARTING MODEL: 2AS8 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.39 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.14 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PROTEIN SOLUTION: 0.5M L-ARGININE, REMARK 280 0.12M LI SULFATE, 0.004M EDTA, 0.1M CAPS, PH 10.5, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 293K, PH 10.50 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y,X,Z+1/4 REMARK 290 4555 Y,-X,Z+3/4 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 38.87150 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 19.43575 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 58.30725 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3 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 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 350 REMARK 350 BIOMOLECULE: 3 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: C 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 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 C 5 CG CD NE CZ NH1 NH2 REMARK 470 ASN C 7 CG OD1 ND2 REMARK 470 VAL C 9 CG1 CG2 REMARK 470 ASN C 10 CG OD1 ND2 REMARK 470 GLU C 14 CG CD OE1 OE2 REMARK 470 GLN C 69 CG CD OE1 NE2 REMARK 470 ARG C 100 CG CD NE CZ NH1 NH2 REMARK 470 GLN C 103 CG CD OE1 NE2 REMARK 470 ARG C 105 CG CD NE CZ NH1 NH2 REMARK 470 ARG C 106 CG CD NE CZ NH1 NH2 REMARK 470 ASN C 108 CG OD1 ND2 REMARK 470 LYS C 126 CG CD CE NZ REMARK 470 ARG C 149 CG CD NE CZ NH1 NH2 REMARK 470 ARG C 157 CG CD NE CZ NH1 NH2 REMARK 470 GLN C 182 CG CD OE1 NE2 REMARK 470 MET C 223 O 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 ND2 ASN B 53 O5 NAG B 301 2.15 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 ND2 ASN A 7 OG SER B 115 2455 2.06 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 HIS A 70 54.69 -161.15 REMARK 500 TYR A 95 76.35 -154.77 REMARK 500 ASP A 163 88.71 -150.51 REMARK 500 ASP A 194 172.44 72.28 REMARK 500 HIS B 70 54.28 -160.03 REMARK 500 TYR B 95 76.22 -156.17 REMARK 500 ASP B 163 87.64 -152.43 REMARK 500 ASP B 163 87.64 -151.02 REMARK 500 TYR B 166 -64.87 -101.41 REMARK 500 ASP B 194 172.81 72.20 REMARK 500 HIS C 70 55.03 -160.81 REMARK 500 TYR C 95 75.89 -156.95 REMARK 500 ASP C 194 172.19 72.13 REMARK 500 MET C 213 19.65 59.13 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 B 518 DISTANCE = 6.17 ANGSTROMS REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5VPG RELATED DB: PDB REMARK 900 RELATED ID: 5VPH RELATED DB: PDB REMARK 900 RELATED ID: 5VPL RELATED DB: PDB DBREF 5VPK A 1 223 UNP I2CMD3 I2CMD3_DERFA 83 305 DBREF 5VPK B 1 223 UNP I2CMD3 I2CMD3_DERFA 83 305 DBREF 5VPK C 1 223 UNP I2CMD3 I2CMD3_DERFA 83 305 SEQRES 1 A 223 THR SER ALA CYS ARG ILE ASN SER VAL ASN VAL PRO SER SEQRES 2 A 223 GLU LEU ASP LEU ARG SER LEU ARG THR VAL THR PRO ILE SEQRES 3 A 223 ARG MET GLN GLY GLY CYS GLY SER CYS TRP ALA PHE SER SEQRES 4 A 223 GLY VAL ALA ALA THR GLU SER ALA TYR LEU ALA TYR ARG SEQRES 5 A 223 ASN THR SER LEU ASP LEU SER GLU GLN GLU LEU VAL ASP SEQRES 6 A 223 CYS ALA SER GLN HIS GLY CYS HIS GLY ASP THR ILE PRO SEQRES 7 A 223 ARG GLY ILE GLU TYR ILE GLN GLN ASN GLY VAL VAL GLU SEQRES 8 A 223 GLU ARG SER TYR PRO TYR VAL ALA ARG GLU GLN GLN CYS SEQRES 9 A 223 ARG ARG PRO ASN SER GLN HIS TYR GLY ILE SER ASN TYR SEQRES 10 A 223 CYS GLN ILE TYR PRO PRO ASP VAL LYS GLN ILE ARG GLU SEQRES 11 A 223 ALA LEU THR GLN THR HIS THR ALA ILE ALA VAL ILE ILE SEQRES 12 A 223 GLY ILE LYS ASP LEU ARG ALA PHE GLN HIS TYR ASP GLY SEQRES 13 A 223 ARG THR ILE ILE GLN HIS ASP ASN GLY TYR GLN PRO ASN SEQRES 14 A 223 TYR HIS ALA VAL ASN ILE VAL GLY TYR GLY SER THR GLN SEQRES 15 A 223 GLY VAL ASP TYR TRP ILE VAL ARG ASN SER TRP ASP THR SEQRES 16 A 223 THR TRP GLY ASP SER GLY TYR GLY TYR PHE GLN ALA GLY SEQRES 17 A 223 ASN ASN LEU MET MET ILE GLU GLN TYR PRO TYR VAL VAL SEQRES 18 A 223 ILE MET SEQRES 1 B 223 THR SER ALA CYS ARG ILE ASN SER VAL ASN VAL PRO SER SEQRES 2 B 223 GLU LEU ASP LEU ARG SER LEU ARG THR VAL THR PRO ILE SEQRES 3 B 223 ARG MET GLN GLY GLY CYS GLY SER CYS TRP ALA PHE SER SEQRES 4 B 223 GLY VAL ALA ALA THR GLU SER ALA TYR LEU ALA TYR ARG SEQRES 5 B 223 ASN THR SER LEU ASP LEU SER GLU GLN GLU LEU VAL ASP SEQRES 6 B 223 CYS ALA SER GLN HIS GLY CYS HIS GLY ASP THR ILE PRO SEQRES 7 B 223 ARG GLY ILE GLU TYR ILE GLN GLN ASN GLY VAL VAL GLU SEQRES 8 B 223 GLU ARG SER TYR PRO TYR VAL ALA ARG GLU GLN GLN CYS SEQRES 9 B 223 ARG ARG PRO ASN SER GLN HIS TYR GLY ILE SER ASN TYR SEQRES 10 B 223 CYS GLN ILE TYR PRO PRO ASP VAL LYS GLN ILE ARG GLU SEQRES 11 B 223 ALA LEU THR GLN THR HIS THR ALA ILE ALA VAL ILE ILE SEQRES 12 B 223 GLY ILE LYS ASP LEU ARG ALA PHE GLN HIS TYR ASP GLY SEQRES 13 B 223 ARG THR ILE ILE GLN HIS ASP ASN GLY TYR GLN PRO ASN SEQRES 14 B 223 TYR HIS ALA VAL ASN ILE VAL GLY TYR GLY SER THR GLN SEQRES 15 B 223 GLY VAL ASP TYR TRP ILE VAL ARG ASN SER TRP ASP THR SEQRES 16 B 223 THR TRP GLY ASP SER GLY TYR GLY TYR PHE GLN ALA GLY SEQRES 17 B 223 ASN ASN LEU MET MET ILE GLU GLN TYR PRO TYR VAL VAL SEQRES 18 B 223 ILE MET SEQRES 1 C 223 THR SER ALA CYS ARG ILE ASN SER VAL ASN VAL PRO SER SEQRES 2 C 223 GLU LEU ASP LEU ARG SER LEU ARG THR VAL THR PRO ILE SEQRES 3 C 223 ARG MET GLN GLY GLY CYS GLY SER CYS TRP ALA PHE SER SEQRES 4 C 223 GLY VAL ALA ALA THR GLU SER ALA TYR LEU ALA TYR ARG SEQRES 5 C 223 ASN THR SER LEU ASP LEU SER GLU GLN GLU LEU VAL ASP SEQRES 6 C 223 CYS ALA SER GLN HIS GLY CYS HIS GLY ASP THR ILE PRO SEQRES 7 C 223 ARG GLY ILE GLU TYR ILE GLN GLN ASN GLY VAL VAL GLU SEQRES 8 C 223 GLU ARG SER TYR PRO TYR VAL ALA ARG GLU GLN GLN CYS SEQRES 9 C 223 ARG ARG PRO ASN SER GLN HIS TYR GLY ILE SER ASN TYR SEQRES 10 C 223 CYS GLN ILE TYR PRO PRO ASP VAL LYS GLN ILE ARG GLU SEQRES 11 C 223 ALA LEU THR GLN THR HIS THR ALA ILE ALA VAL ILE ILE SEQRES 12 C 223 GLY ILE LYS ASP LEU ARG ALA PHE GLN HIS TYR ASP GLY SEQRES 13 C 223 ARG THR ILE ILE GLN HIS ASP ASN GLY TYR GLN PRO ASN SEQRES 14 C 223 TYR HIS ALA VAL ASN ILE VAL GLY TYR GLY SER THR GLN SEQRES 15 C 223 GLY VAL ASP TYR TRP ILE VAL ARG ASN SER TRP ASP THR SEQRES 16 C 223 THR TRP GLY ASP SER GLY TYR GLY TYR PHE GLN ALA GLY SEQRES 17 C 223 ASN ASN LEU MET MET ILE GLU GLN TYR PRO TYR VAL VAL SEQRES 18 C 223 ILE MET HET SO4 A 301 5 HET SO4 A 302 5 HET NAG A 303 14 HET SO4 A 304 5 HET SO4 A 305 5 HET SO4 A 306 5 HET NAG B 301 14 HET SO4 B 302 5 HETNAM SO4 SULFATE ION HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETSYN NAG N-ACETYL-BETA-D-GLUCOSAMINE; 2-ACETAMIDO-2-DEOXY-BETA- HETSYN 2 NAG D-GLUCOSE; 2-ACETAMIDO-2-DEOXY-D-GLUCOSE; 2-ACETAMIDO- HETSYN 3 NAG 2-DEOXY-GLUCOSE; N-ACETYL-D-GLUCOSAMINE FORMUL 4 SO4 6(O4 S 2-) FORMUL 6 NAG 2(C8 H15 N O6) FORMUL 12 HOH *289(H2 O) HELIX 1 AA1 LEU A 17 ARG A 21 1 5 HELIX 2 AA2 SER A 34 ASN A 53 1 20 HELIX 3 AA3 SER A 59 ALA A 67 1 9 HELIX 4 AA4 THR A 76 GLY A 88 1 13 HELIX 5 AA5 GLU A 91 TYR A 95 5 5 HELIX 6 AA6 ASP A 124 HIS A 136 1 13 HELIX 7 AA7 ASP A 147 HIS A 153 1 7 HELIX 8 AA8 ASN A 210 ILE A 214 5 5 HELIX 9 AA9 LEU B 17 ARG B 21 1 5 HELIX 10 AB1 SER B 34 ASN B 53 1 20 HELIX 11 AB2 SER B 59 ALA B 67 1 9 HELIX 12 AB3 HIS B 70 GLY B 74 5 5 HELIX 13 AB4 THR B 76 GLY B 88 1 13 HELIX 14 AB5 GLU B 91 TYR B 95 5 5 HELIX 15 AB6 ASP B 124 HIS B 136 1 13 HELIX 16 AB7 ASP B 147 HIS B 153 1 7 HELIX 17 AB8 ASN B 210 ILE B 214 5 5 HELIX 18 AB9 LEU C 17 ARG C 21 1 5 HELIX 19 AC1 SER C 34 ASN C 53 1 20 HELIX 20 AC2 SER C 59 ALA C 67 1 9 HELIX 21 AC3 THR C 76 GLY C 88 1 13 HELIX 22 AC4 GLU C 91 TYR C 95 5 5 HELIX 23 AC5 ASP C 124 HIS C 136 1 13 HELIX 24 AC6 ASP C 147 HIS C 153 1 7 HELIX 25 AC7 ASN C 210 ILE C 214 5 5 SHEET 1 AA1 3 LEU A 15 ASP A 16 0 SHEET 2 AA1 3 ASN A 169 THR A 181 -1 O TYR A 178 N LEU A 15 SHEET 3 AA1 3 ILE A 139 ILE A 145 -1 N ILE A 143 O HIS A 171 SHEET 1 AA2 4 LEU A 15 ASP A 16 0 SHEET 2 AA2 4 ASN A 169 THR A 181 -1 O TYR A 178 N LEU A 15 SHEET 3 AA2 4 VAL A 184 ARG A 190 -1 O ILE A 188 N VAL A 176 SHEET 4 AA2 4 TYR A 202 GLN A 206 -1 O PHE A 205 N TRP A 187 SHEET 1 AA3 2 ASN A 116 GLN A 119 0 SHEET 2 AA3 2 TYR A 219 ILE A 222 -1 O ILE A 222 N ASN A 116 SHEET 1 AA4 3 LEU B 15 ASP B 16 0 SHEET 2 AA4 3 ASN B 169 THR B 181 -1 O TYR B 178 N LEU B 15 SHEET 3 AA4 3 ILE B 139 ILE B 145 -1 N ILE B 143 O HIS B 171 SHEET 1 AA5 4 LEU B 15 ASP B 16 0 SHEET 2 AA5 4 ASN B 169 THR B 181 -1 O TYR B 178 N LEU B 15 SHEET 3 AA5 4 VAL B 184 ARG B 190 -1 O ILE B 188 N VAL B 176 SHEET 4 AA5 4 TYR B 202 GLN B 206 -1 O PHE B 205 N TRP B 187 SHEET 1 AA6 2 ASN B 116 GLN B 119 0 SHEET 2 AA6 2 TYR B 219 ILE B 222 -1 O ILE B 222 N ASN B 116 SHEET 1 AA7 3 LEU C 15 ASP C 16 0 SHEET 2 AA7 3 ASN C 169 THR C 181 -1 O TYR C 178 N LEU C 15 SHEET 3 AA7 3 ILE C 139 ILE C 145 -1 N ILE C 143 O HIS C 171 SHEET 1 AA8 4 LEU C 15 ASP C 16 0 SHEET 2 AA8 4 ASN C 169 THR C 181 -1 O TYR C 178 N LEU C 15 SHEET 3 AA8 4 VAL C 184 ARG C 190 -1 O ILE C 188 N VAL C 176 SHEET 4 AA8 4 TYR C 202 GLN C 206 -1 O PHE C 205 N TRP C 187 SHEET 1 AA9 2 ASN C 116 GLN C 119 0 SHEET 2 AA9 2 TYR C 219 ILE C 222 -1 O ILE C 222 N ASN C 116 SSBOND 1 CYS A 4 CYS A 118 1555 1555 2.06 SSBOND 2 CYS A 32 CYS A 72 1555 1555 2.04 SSBOND 3 CYS A 66 CYS A 104 1555 1555 2.06 SSBOND 4 CYS B 4 CYS B 118 1555 1555 2.05 SSBOND 5 CYS B 32 CYS B 72 1555 1555 2.03 SSBOND 6 CYS B 66 CYS B 104 1555 1555 2.07 SSBOND 7 CYS C 4 CYS C 118 1555 1555 2.09 SSBOND 8 CYS C 32 CYS C 72 1555 1555 2.07 SSBOND 9 CYS C 66 CYS C 104 1555 1555 2.05 LINK ND2 ASN A 53 C1 NAG A 303 1555 1555 1.44 LINK ND2 ASN B 53 C1 NAG B 301 1555 1555 1.42 CISPEP 1 TYR A 121 PRO A 122 0 -10.73 CISPEP 2 TYR B 121 PRO B 122 0 -9.33 CISPEP 3 TYR C 121 PRO C 122 0 -9.68 CRYST1 91.159 91.159 77.743 90.00 90.00 90.00 P 41 12 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 0.010970 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010970 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012863 0.00000