HEADER ANTIMICROBIAL PROTEIN 05-JUN-18 6DMQ TITLE CRYSTAL STRUCTURE OF THE T27A MUTANT OF HUMAN ALPHA DEFENSIN HNP4. COMPND MOL_ID: 1; COMPND 2 MOLECULE: NEUTROPHIL DEFENSIN 4; COMPND 3 CHAIN: A, B, C, D, E, F, G, H; COMPND 4 SYNONYM: DEFENSIN,ALPHA 4,HNP-4,HP-4; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 4 ORGANISM_COMMON: HUMAN; SOURCE 5 ORGANISM_TAXID: 9606 KEYWDS HUMAN ALPHA-DEFENSIN, ANTIMICROBIAL PEPTIDE, ANTIMICROBIAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR N.GOHAIN,W.D.TOLBERT,M.PAZGIER REVDAT 3 11-OCT-23 6DMQ 1 JRNL REVDAT 2 20-FEB-19 6DMQ 1 JRNL REVDAT 1 30-JAN-19 6DMQ 0 JRNL AUTH H.HU,B.DI,W.D.TOLBERT,N.GOHAIN,W.YUAN,P.GAO,B.MA,Q.HE, JRNL AUTH 2 M.PAZGIER,L.ZHAO,W.LU JRNL TITL SYSTEMATIC MUTATIONAL ANALYSIS OF HUMAN NEUTROPHIL JRNL TITL 2 ALPHA-DEFENSIN HNP4. JRNL REF BIOCHIM BIOPHYS ACTA V.1861 835 2019 JRNL REF 2 BIOMEMBR JRNL REFN ESSN 1879-2642 JRNL PMID 30658057 JRNL DOI 10.1016/J.BBAMEM.2019.01.007 REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0222 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) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.73 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 26124 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) : 0.271 REMARK 3 R VALUE (WORKING SET) : 0.269 REMARK 3 FREE R VALUE : 0.310 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1383 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) : 1.70 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.74 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1870 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.55 REMARK 3 BIN R VALUE (WORKING SET) : 0.1790 REMARK 3 BIN FREE R VALUE SET COUNT : 105 REMARK 3 BIN FREE R VALUE : 0.2390 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1940 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 8 REMARK 3 SOLVENT ATOMS : 172 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.97 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.88000 REMARK 3 B22 (A**2) : -2.76000 REMARK 3 B33 (A**2) : 0.88000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.13000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.035 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.033 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.040 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.123 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.924 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.891 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2049 ; 0.017 ; 0.014 REMARK 3 BOND LENGTHS OTHERS (A): 1816 ; 0.001 ; 0.017 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2768 ; 1.967 ; 1.667 REMARK 3 BOND ANGLES OTHERS (DEGREES): 4249 ; 0.973 ; 1.639 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 259 ; 8.857 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 120 ;27.430 ;14.667 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 349 ;15.751 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 40 ;18.766 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 263 ; 0.084 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2345 ; 0.013 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 411 ; 0.003 ; 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): 1042 ; 1.286 ; 1.636 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1041 ; 1.285 ; 1.635 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1299 ; 1.889 ; 2.443 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1300 ; 1.888 ; 2.443 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1007 ; 1.448 ; 1.841 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1008 ; 1.449 ; 1.843 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 1470 ; 2.076 ; 2.714 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 2117 ; 4.737 ;19.840 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 2092 ; 4.710 ;19.563 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 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 8 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 32 REMARK 3 ORIGIN FOR THE GROUP (A): 7.4976 2.0968 40.0893 REMARK 3 T TENSOR REMARK 3 T11: 0.0443 T22: 0.1132 REMARK 3 T33: 0.0576 T12: -0.0180 REMARK 3 T13: 0.0213 T23: -0.0205 REMARK 3 L TENSOR REMARK 3 L11: 2.2662 L22: 5.7870 REMARK 3 L33: 3.0667 L12: -1.0948 REMARK 3 L13: -0.5845 L23: -0.4933 REMARK 3 S TENSOR REMARK 3 S11: -0.0481 S12: -0.2182 S13: -0.1965 REMARK 3 S21: 0.2609 S22: -0.0048 S23: 0.4137 REMARK 3 S31: 0.2779 S32: -0.1202 S33: 0.0528 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 32 REMARK 3 ORIGIN FOR THE GROUP (A): 12.9563 -2.2104 26.9290 REMARK 3 T TENSOR REMARK 3 T11: 0.0280 T22: 0.0727 REMARK 3 T33: 0.0206 T12: 0.0006 REMARK 3 T13: -0.0185 T23: -0.0033 REMARK 3 L TENSOR REMARK 3 L11: 3.3706 L22: 3.5683 REMARK 3 L33: 3.4286 L12: -0.2114 REMARK 3 L13: 0.9886 L23: 0.4338 REMARK 3 S TENSOR REMARK 3 S11: 0.0426 S12: 0.1034 S13: 0.0552 REMARK 3 S21: -0.3091 S22: -0.0528 S23: 0.2244 REMARK 3 S31: 0.0187 S32: -0.0904 S33: 0.0101 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 31 REMARK 3 ORIGIN FOR THE GROUP (A): -5.9748 -16.7632 39.0615 REMARK 3 T TENSOR REMARK 3 T11: 0.0306 T22: 0.1035 REMARK 3 T33: 0.0413 T12: -0.0272 REMARK 3 T13: -0.0007 T23: -0.0151 REMARK 3 L TENSOR REMARK 3 L11: 1.7770 L22: 5.8382 REMARK 3 L33: 2.5393 L12: -0.0369 REMARK 3 L13: 1.3177 L23: 0.7669 REMARK 3 S TENSOR REMARK 3 S11: -0.0797 S12: -0.1007 S13: 0.2045 REMARK 3 S21: 0.0776 S22: 0.0421 S23: -0.2437 REMARK 3 S31: -0.2425 S32: 0.1948 S33: 0.0376 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : D 1 D 32 REMARK 3 ORIGIN FOR THE GROUP (A): -13.5821 -11.9075 27.0309 REMARK 3 T TENSOR REMARK 3 T11: 0.0212 T22: 0.0764 REMARK 3 T33: 0.0224 T12: -0.0106 REMARK 3 T13: -0.0057 T23: 0.0007 REMARK 3 L TENSOR REMARK 3 L11: 1.1644 L22: 2.5762 REMARK 3 L33: 6.1007 L12: -0.4106 REMARK 3 L13: -0.9056 L23: -1.9318 REMARK 3 S TENSOR REMARK 3 S11: 0.0072 S12: 0.0284 S13: -0.1423 REMARK 3 S21: -0.2116 S22: 0.0108 S23: 0.0638 REMARK 3 S31: 0.2559 S32: 0.0684 S33: -0.0181 REMARK 3 REMARK 3 TLS GROUP : 5 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : E 1 E 31 REMARK 3 ORIGIN FOR THE GROUP (A): 4.9286 2.6016 -6.1292 REMARK 3 T TENSOR REMARK 3 T11: 0.0575 T22: 0.1238 REMARK 3 T33: 0.0524 T12: 0.0206 REMARK 3 T13: 0.0235 T23: 0.0100 REMARK 3 L TENSOR REMARK 3 L11: 1.7018 L22: 5.6703 REMARK 3 L33: 2.0006 L12: 1.0150 REMARK 3 L13: -0.3975 L23: 0.6066 REMARK 3 S TENSOR REMARK 3 S11: -0.0354 S12: 0.1730 S13: -0.1766 REMARK 3 S21: -0.2598 S22: 0.0276 S23: -0.4850 REMARK 3 S31: 0.2466 S32: 0.1526 S33: 0.0078 REMARK 3 REMARK 3 TLS GROUP : 6 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : F 1 F 32 REMARK 3 ORIGIN FOR THE GROUP (A): -0.6206 -2.2629 6.6750 REMARK 3 T TENSOR REMARK 3 T11: 0.0190 T22: 0.0751 REMARK 3 T33: 0.0261 T12: -0.0008 REMARK 3 T13: -0.0137 T23: -0.0012 REMARK 3 L TENSOR REMARK 3 L11: 2.5029 L22: 3.3037 REMARK 3 L33: 4.3832 L12: 0.3894 REMARK 3 L13: 0.9062 L23: -0.5114 REMARK 3 S TENSOR REMARK 3 S11: 0.0055 S12: -0.0891 S13: 0.1234 REMARK 3 S21: 0.2324 S22: -0.0577 S23: -0.1971 REMARK 3 S31: 0.0335 S32: 0.0484 S33: 0.0522 REMARK 3 REMARK 3 TLS GROUP : 7 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : G 1 G 31 REMARK 3 ORIGIN FOR THE GROUP (A): 18.3140 -16.7530 -5.4556 REMARK 3 T TENSOR REMARK 3 T11: 0.0234 T22: 0.0911 REMARK 3 T33: 0.0297 T12: 0.0218 REMARK 3 T13: -0.0055 T23: 0.0184 REMARK 3 L TENSOR REMARK 3 L11: 2.0170 L22: 5.8763 REMARK 3 L33: 2.6037 L12: 0.3311 REMARK 3 L13: 1.0616 L23: -0.9764 REMARK 3 S TENSOR REMARK 3 S11: -0.1073 S12: 0.0911 S13: 0.2228 REMARK 3 S21: -0.0837 S22: 0.0875 S23: 0.1255 REMARK 3 S31: -0.2174 S32: -0.2135 S33: 0.0197 REMARK 3 REMARK 3 TLS GROUP : 8 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : H 1 H 31 REMARK 3 ORIGIN FOR THE GROUP (A): 26.2235 -11.9390 6.1771 REMARK 3 T TENSOR REMARK 3 T11: 0.0106 T22: 0.0693 REMARK 3 T33: 0.0233 T12: 0.0064 REMARK 3 T13: -0.0099 T23: 0.0012 REMARK 3 L TENSOR REMARK 3 L11: 0.5367 L22: 2.2665 REMARK 3 L33: 5.5521 L12: 0.3876 REMARK 3 L13: -0.6568 L23: 2.0941 REMARK 3 S TENSOR REMARK 3 S11: 0.0307 S12: -0.0221 S13: -0.0695 REMARK 3 S21: 0.1379 S22: 0.0338 S23: -0.0631 REMARK 3 S31: 0.1532 S32: -0.0078 S33: -0.0645 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 6DMQ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-JUN-18. REMARK 100 THE DEPOSITION ID IS D_1000234929. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-JAN-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL14-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97946 REMARK 200 MONOCHROMATOR : SI (111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 325 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 27445 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 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 (%) : 99.7 REMARK 200 DATA REDUNDANCY : 3.600 REMARK 200 R MERGE (I) : 0.09800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.7000 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) : 1.73 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 3.60 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 1ZMM REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.96 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.12 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30% MPD 15% PEG 8000 100 MM SODIUM REMARK 280 ACETATE PH 5.5 100 MM CALCIUM CHLORIDE, VAPOR DIFFUSION, SITTING REMARK 280 DROP, TEMPERATURE 294K 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 19.49450 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3, 4 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 620 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 4850 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -4.0 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 880 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 4700 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -12.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, D 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 640 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 4750 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -5.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: E, F 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: 4 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 620 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 4470 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -5.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: G, H 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 33 REMARK 465 ARG C 32 REMARK 465 VAL C 33 REMARK 465 ARG E 32 REMARK 465 VAL E 33 REMARK 465 ARG G 32 REMARK 465 VAL G 33 REMARK 465 ARG H 32 REMARK 465 VAL H 33 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 A 18 O HOH A 101 2.03 REMARK 500 OG1 THR C 12 O HOH C 201 2.04 REMARK 500 O HOH C 201 O HOH C 225 2.09 REMARK 500 O HOH B 103 O HOH B 108 2.10 REMARK 500 NH2 ARG G 15 O HOH G 101 2.11 REMARK 500 O HOH C 216 O HOH D 119 2.13 REMARK 500 O HOH D 105 O HOH D 110 2.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 GLU F 13 CD GLU F 13 OE2 -0.067 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 ARG F 5 NE - CZ - NH1 ANGL. DEV. = -3.4 DEGREES REMARK 500 ARG G 5 NE - CZ - NH2 ANGL. DEV. = -3.5 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 VAL A 7 -85.08 -124.23 REMARK 500 VAL B 7 -70.31 76.94 REMARK 500 VAL C 7 -82.64 -128.93 REMARK 500 VAL D 7 -66.97 81.55 REMARK 500 ARG D 32 -146.21 -54.57 REMARK 500 VAL E 7 -81.45 -128.08 REMARK 500 VAL F 7 -70.78 80.07 REMARK 500 VAL G 7 -81.89 -129.96 REMARK 500 VAL H 7 -65.77 74.49 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG A 11 0.20 SIDE CHAIN REMARK 500 ARG B 10 0.12 SIDE CHAIN REMARK 500 ARG C 10 0.12 SIDE CHAIN REMARK 500 ARG D 15 0.15 SIDE CHAIN REMARK 500 ARG D 32 0.10 SIDE CHAIN REMARK 500 ARG E 15 0.13 SIDE CHAIN REMARK 500 ARG F 11 0.09 SIDE CHAIN REMARK 500 ARG F 15 0.12 SIDE CHAIN REMARK 500 ARG G 10 0.08 SIDE CHAIN REMARK 500 ARG G 11 0.12 SIDE CHAIN 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 G 125 DISTANCE = 6.62 ANGSTROMS REMARK 525 HOH G 126 DISTANCE = 8.34 ANGSTROMS REMARK 525 HOH G 127 DISTANCE = 8.96 ANGSTROMS REMARK 525 HOH H 126 DISTANCE = 7.29 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MPD C 101 DBREF 6DMQ A 1 33 UNP P12838 DEF4_HUMAN 64 96 DBREF 6DMQ B 1 33 UNP P12838 DEF4_HUMAN 64 96 DBREF 6DMQ C 1 33 UNP P12838 DEF4_HUMAN 64 96 DBREF 6DMQ D 1 33 UNP P12838 DEF4_HUMAN 64 96 DBREF 6DMQ E 1 33 UNP P12838 DEF4_HUMAN 64 96 DBREF 6DMQ F 1 33 UNP P12838 DEF4_HUMAN 64 96 DBREF 6DMQ G 1 33 UNP P12838 DEF4_HUMAN 64 96 DBREF 6DMQ H 1 33 UNP P12838 DEF4_HUMAN 64 96 SEQADV 6DMQ ALA A 27 UNP P12838 THR 90 ENGINEERED MUTATION SEQADV 6DMQ ALA B 27 UNP P12838 THR 90 ENGINEERED MUTATION SEQADV 6DMQ ALA C 27 UNP P12838 THR 90 ENGINEERED MUTATION SEQADV 6DMQ ALA D 27 UNP P12838 THR 90 ENGINEERED MUTATION SEQADV 6DMQ ALA E 27 UNP P12838 THR 90 ENGINEERED MUTATION SEQADV 6DMQ ALA F 27 UNP P12838 THR 90 ENGINEERED MUTATION SEQADV 6DMQ ALA G 27 UNP P12838 THR 90 ENGINEERED MUTATION SEQADV 6DMQ ALA H 27 UNP P12838 THR 90 ENGINEERED MUTATION SEQRES 1 A 33 VAL CYS SER CYS ARG LEU VAL PHE CYS ARG ARG THR GLU SEQRES 2 A 33 LEU ARG VAL GLY ASN CYS LEU ILE GLY GLY VAL SER PHE SEQRES 3 A 33 ALA TYR CYS CYS THR ARG VAL SEQRES 1 B 33 VAL CYS SER CYS ARG LEU VAL PHE CYS ARG ARG THR GLU SEQRES 2 B 33 LEU ARG VAL GLY ASN CYS LEU ILE GLY GLY VAL SER PHE SEQRES 3 B 33 ALA TYR CYS CYS THR ARG VAL SEQRES 1 C 33 VAL CYS SER CYS ARG LEU VAL PHE CYS ARG ARG THR GLU SEQRES 2 C 33 LEU ARG VAL GLY ASN CYS LEU ILE GLY GLY VAL SER PHE SEQRES 3 C 33 ALA TYR CYS CYS THR ARG VAL SEQRES 1 D 33 VAL CYS SER CYS ARG LEU VAL PHE CYS ARG ARG THR GLU SEQRES 2 D 33 LEU ARG VAL GLY ASN CYS LEU ILE GLY GLY VAL SER PHE SEQRES 3 D 33 ALA TYR CYS CYS THR ARG VAL SEQRES 1 E 33 VAL CYS SER CYS ARG LEU VAL PHE CYS ARG ARG THR GLU SEQRES 2 E 33 LEU ARG VAL GLY ASN CYS LEU ILE GLY GLY VAL SER PHE SEQRES 3 E 33 ALA TYR CYS CYS THR ARG VAL SEQRES 1 F 33 VAL CYS SER CYS ARG LEU VAL PHE CYS ARG ARG THR GLU SEQRES 2 F 33 LEU ARG VAL GLY ASN CYS LEU ILE GLY GLY VAL SER PHE SEQRES 3 F 33 ALA TYR CYS CYS THR ARG VAL SEQRES 1 G 33 VAL CYS SER CYS ARG LEU VAL PHE CYS ARG ARG THR GLU SEQRES 2 G 33 LEU ARG VAL GLY ASN CYS LEU ILE GLY GLY VAL SER PHE SEQRES 3 G 33 ALA TYR CYS CYS THR ARG VAL SEQRES 1 H 33 VAL CYS SER CYS ARG LEU VAL PHE CYS ARG ARG THR GLU SEQRES 2 H 33 LEU ARG VAL GLY ASN CYS LEU ILE GLY GLY VAL SER PHE SEQRES 3 H 33 ALA TYR CYS CYS THR ARG VAL HET MPD C 101 8 HETNAM MPD (4S)-2-METHYL-2,4-PENTANEDIOL FORMUL 9 MPD C6 H14 O2 FORMUL 10 HOH *172(H2 O) SHEET 1 AA1 6 CYS A 2 ARG A 5 0 SHEET 2 AA1 6 VAL A 24 THR A 31 -1 O ALA A 27 N ARG A 5 SHEET 3 AA1 6 GLU A 13 ILE A 21 -1 N LEU A 14 O CYS A 30 SHEET 4 AA1 6 LEU B 14 ILE B 21 -1 O LEU B 20 N ASN A 18 SHEET 5 AA1 6 VAL B 24 CYS B 30 -1 O CYS B 30 N LEU B 14 SHEET 6 AA1 6 CYS B 2 ARG B 5 -1 N ARG B 5 O ALA B 27 SHEET 1 AA2 6 CYS C 2 ARG C 5 0 SHEET 2 AA2 6 VAL C 24 CYS C 30 -1 O CYS C 29 N SER C 3 SHEET 3 AA2 6 LEU C 14 ILE C 21 -1 N GLY C 17 O TYR C 28 SHEET 4 AA2 6 GLU D 13 ILE D 21 -1 O LEU D 20 N ASN C 18 SHEET 5 AA2 6 VAL D 24 THR D 31 -1 O PHE D 26 N CYS D 19 SHEET 6 AA2 6 CYS D 2 ARG D 5 -1 N ARG D 5 O ALA D 27 SHEET 1 AA3 6 CYS E 2 ARG E 5 0 SHEET 2 AA3 6 VAL E 24 CYS E 30 -1 O CYS E 29 N SER E 3 SHEET 3 AA3 6 LEU E 14 ILE E 21 -1 N LEU E 14 O CYS E 30 SHEET 4 AA3 6 LEU F 14 ILE F 21 -1 O ASN F 18 N LEU E 20 SHEET 5 AA3 6 VAL F 24 CYS F 30 -1 O TYR F 28 N GLY F 17 SHEET 6 AA3 6 CYS F 2 ARG F 5 -1 N ARG F 5 O ALA F 27 SHEET 1 AA4 6 CYS G 2 ARG G 5 0 SHEET 2 AA4 6 VAL G 24 CYS G 30 -1 O ALA G 27 N ARG G 5 SHEET 3 AA4 6 LEU G 14 ILE G 21 -1 N LEU G 14 O CYS G 30 SHEET 4 AA4 6 LEU H 14 ILE H 21 -1 O LEU H 20 N ASN G 18 SHEET 5 AA4 6 VAL H 24 CYS H 30 -1 O TYR H 28 N GLY H 17 SHEET 6 AA4 6 CYS H 2 ARG H 5 -1 N SER H 3 O CYS H 29 SSBOND 1 CYS A 2 CYS A 30 1555 1555 2.07 SSBOND 2 CYS A 4 CYS A 19 1555 1555 2.02 SSBOND 3 CYS A 9 CYS A 29 1555 1555 1.96 SSBOND 4 CYS B 2 CYS B 30 1555 1555 2.06 SSBOND 5 CYS B 4 CYS B 19 1555 1555 2.00 SSBOND 6 CYS B 9 CYS B 29 1555 1555 2.03 SSBOND 7 CYS C 2 CYS C 30 1555 1555 2.07 SSBOND 8 CYS C 4 CYS C 19 1555 1555 2.03 SSBOND 9 CYS C 9 CYS C 29 1555 1555 2.05 SSBOND 10 CYS D 2 CYS D 30 1555 1555 2.03 SSBOND 11 CYS D 4 CYS D 19 1555 1555 2.10 SSBOND 12 CYS D 9 CYS D 29 1555 1555 1.97 SSBOND 13 CYS E 2 CYS E 30 1555 1555 2.06 SSBOND 14 CYS E 4 CYS E 19 1555 1555 1.98 SSBOND 15 CYS E 9 CYS E 29 1555 1555 2.01 SSBOND 16 CYS F 2 CYS F 30 1555 1555 2.01 SSBOND 17 CYS F 4 CYS F 19 1555 1555 2.07 SSBOND 18 CYS F 9 CYS F 29 1555 1555 1.96 SSBOND 19 CYS G 2 CYS G 30 1555 1555 2.05 SSBOND 20 CYS G 4 CYS G 19 1555 1555 2.04 SSBOND 21 CYS G 9 CYS G 29 1555 1555 2.06 SSBOND 22 CYS H 2 CYS H 30 1555 1555 2.04 SSBOND 23 CYS H 4 CYS H 19 1555 1555 2.05 SSBOND 24 CYS H 9 CYS H 29 1555 1555 2.08 SITE 1 AC1 6 ARG C 15 VAL C 16 GLY C 17 ASN C 18 SITE 2 AC1 6 HOH C 210 HOH C 215 CRYST1 47.704 38.989 71.130 90.00 108.93 90.00 P 1 21 1 16 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 0.020963 0.000000 0.007189 0.00000 SCALE2 0.000000 0.025648 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014863 0.00000