HEADER METAL BINDING PROTEIN/PROTEIN BINDING 13-JAN-17 5WYH TITLE CRYSTAL STRUCTURE OF RIDL(1-200) COMPLEXED WITH VPS29 COMPND MOL_ID: 1; COMPND 2 MOLECULE: VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 29; COMPND 3 CHAIN: A, C; COMPND 4 SYNONYM: HVPS29,PEP11 HOMOLOG,VESICLE PROTEIN SORTING 29; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: INTERAPTIN; COMPND 8 CHAIN: B, D; COMPND 9 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: VPS29, DC15, DC7, MDS007; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 MOL_ID: 2; SOURCE 10 ORGANISM_SCIENTIFIC: LEGIONELLA PNEUMOPHILA SUBSP. PNEUMOPHILA ATCC SOURCE 11 43290; SOURCE 12 ORGANISM_TAXID: 933093; SOURCE 13 GENE: LP12_2303; SOURCE 14 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 15 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 16 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID KEYWDS COMPLEX VPS29 RIDL, METAL BINDING PROTEIN-PROTEIN BINDING COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR J.YAO,Q.SUN,D.JIA REVDAT 3 20-MAR-24 5WYH 1 REMARK REVDAT 2 23-MAY-18 5WYH 1 JRNL REVDAT 1 24-JAN-18 5WYH 0 JRNL AUTH J.YAO,F.YANG,X.SUN,S.WANG,N.GAN,Q.LIU,D.LIU,X.ZHANG,D.NIU, JRNL AUTH 2 Y.WEI,C.MA,Z.Q.LUO,Q.SUN,D.JIA JRNL TITL MECHANISM OF INHIBITION OF RETROMER TRANSPORT BY THE JRNL TITL 2 BACTERIAL EFFECTOR RIDL. JRNL REF PROC. NATL. ACAD. SCI. V. 115 E1446 2018 JRNL REF 2 U.S.A. JRNL REFN ESSN 1091-6490 JRNL PMID 29386389 JRNL DOI 10.1073/PNAS.1717383115 REMARK 2 REMARK 2 RESOLUTION. 2.46 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 : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.46 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 31.86 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 81.8 REMARK 3 NUMBER OF REFLECTIONS : 31351 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) : 0.191 REMARK 3 R VALUE (WORKING SET) : 0.190 REMARK 3 FREE R VALUE : 0.225 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1665 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) : 2.46 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.52 REMARK 3 REFLECTION IN BIN (WORKING SET) : 400 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 14.30 REMARK 3 BIN R VALUE (WORKING SET) : 0.2430 REMARK 3 BIN FREE R VALUE SET COUNT : 24 REMARK 3 BIN FREE R VALUE : 0.3080 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6147 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 6 REMARK 3 SOLVENT ATOMS : 226 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 52.80 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -13.88000 REMARK 3 B22 (A**2) : 0.95000 REMARK 3 B33 (A**2) : 12.93000 REMARK 3 B12 (A**2) : 0.30000 REMARK 3 B13 (A**2) : -0.19000 REMARK 3 B23 (A**2) : -2.29000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.112 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.057 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.165 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 14.370 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.942 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.918 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6286 ; 0.009 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 5843 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 8488 ; 1.392 ; 1.961 REMARK 3 BOND ANGLES OTHERS (DEGREES): 13622 ; 0.937 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 760 ; 5.774 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 309 ;39.430 ;25.016 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1132 ;16.612 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 28 ;14.560 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 932 ; 0.081 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 6912 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1224 ; 0.001 ; 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): 3052 ; 1.985 ; 2.812 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 3051 ; 1.983 ; 2.812 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3808 ; 3.117 ; 4.215 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 3809 ; 3.117 ; 4.215 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 3234 ; 2.380 ; 3.094 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 3234 ; 2.378 ; 3.095 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 4681 ; 3.771 ; 4.537 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 6969 ; 5.663 ;33.704 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 6946 ; 5.644 ;33.597 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 : 2 REMARK 3 GROUP CHAIN1 RANGE CHAIN2 RANGE COUNT RMS WEIGHT REMARK 3 1 A -2 182 C -2 182 11776 0.06 0.05 REMARK 3 2 B 5 199 D 5 199 12986 0.06 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 : 0.816 REMARK 3 TWIN DOMAIN : 2 REMARK 3 TWIN OPERATOR : H, -H-K, -H-L REMARK 3 TWIN FRACTION : 0.184 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 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 -2 A 182 REMARK 3 ORIGIN FOR THE GROUP (A): 22.6159 -22.2659 15.3991 REMARK 3 T TENSOR REMARK 3 T11: 0.0286 T22: 0.0341 REMARK 3 T33: 0.0996 T12: 0.0122 REMARK 3 T13: 0.0044 T23: -0.0066 REMARK 3 L TENSOR REMARK 3 L11: 3.9704 L22: 4.4010 REMARK 3 L33: 2.7618 L12: 0.3382 REMARK 3 L13: -0.4798 L23: -0.4684 REMARK 3 S TENSOR REMARK 3 S11: -0.0296 S12: -0.3449 S13: 0.1618 REMARK 3 S21: 0.2781 S22: 0.0795 S23: -0.1259 REMARK 3 S31: -0.0585 S32: 0.0186 S33: -0.0499 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 5 B 200 REMARK 3 ORIGIN FOR THE GROUP (A): 1.7037 -59.3687 29.5450 REMARK 3 T TENSOR REMARK 3 T11: 0.3462 T22: 0.2026 REMARK 3 T33: 0.1188 T12: -0.0587 REMARK 3 T13: 0.0124 T23: 0.0839 REMARK 3 L TENSOR REMARK 3 L11: 1.4151 L22: 2.5288 REMARK 3 L33: 3.8363 L12: 0.0667 REMARK 3 L13: 0.1681 L23: -1.4741 REMARK 3 S TENSOR REMARK 3 S11: 0.0886 S12: -0.5208 S13: -0.2857 REMARK 3 S21: 0.4278 S22: -0.0642 S23: -0.0367 REMARK 3 S31: 0.5574 S32: -0.0920 S33: -0.0244 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 -2 C 182 REMARK 3 ORIGIN FOR THE GROUP (A): 0.5185 0.4048 0.1521 REMARK 3 T TENSOR REMARK 3 T11: 0.0475 T22: 0.0279 REMARK 3 T33: 0.0743 T12: -0.0126 REMARK 3 T13: 0.0539 T23: -0.0091 REMARK 3 L TENSOR REMARK 3 L11: 4.3276 L22: 4.5061 REMARK 3 L33: 2.4261 L12: -0.1977 REMARK 3 L13: 0.2683 L23: -0.7991 REMARK 3 S TENSOR REMARK 3 S11: -0.0972 S12: 0.3339 S13: -0.0946 REMARK 3 S21: -0.2525 S22: 0.0780 S23: -0.1597 REMARK 3 S31: 0.0313 S32: 0.0126 S33: 0.0192 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 3 D 200 REMARK 3 ORIGIN FOR THE GROUP (A): -19.9320 37.5791 -14.5043 REMARK 3 T TENSOR REMARK 3 T11: 0.3446 T22: 0.2260 REMARK 3 T33: 0.1110 T12: 0.0061 REMARK 3 T13: 0.0310 T23: 0.0888 REMARK 3 L TENSOR REMARK 3 L11: 1.6780 L22: 3.2468 REMARK 3 L33: 3.6617 L12: -0.4682 REMARK 3 L13: -0.0266 L23: -1.4497 REMARK 3 S TENSOR REMARK 3 S11: 0.0554 S12: 0.5801 S13: 0.3407 REMARK 3 S21: -0.5926 S22: -0.0874 S23: -0.0569 REMARK 3 S31: -0.4567 S32: -0.1487 S33: 0.0320 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 1.10 REMARK 3 SHRINKAGE RADIUS : 1.10 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 5WYH COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 19-JAN-17. REMARK 100 THE DEPOSITION ID IS D_1300002600. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-MAR-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : AICHISR REMARK 200 BEAMLINE : BL2S1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9792 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MAR CCD 130 MM REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 37098 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 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 (%) : 96.6 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : 0.10600 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 10.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.54 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.7 REMARK 200 DATA REDUNDANCY IN SHELL : 3.70 REMARK 200 R MERGE FOR SHELL (I) : 0.89100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 62.31 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.26 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M TRIS PH8.0, 20% PEG 8000, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,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 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 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 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 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 LEU B 3 REMARK 465 GLU B 4 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 LEU A 40 CA - CB - CG ANGL. DEV. = 16.8 DEGREES REMARK 500 LEU C 40 CA - CB - CG ANGL. DEV. = 16.9 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 CYS A 41 -47.43 104.38 REMARK 500 HIS A 115 -40.53 72.94 REMARK 500 THR A 144 -164.74 -103.45 REMARK 500 ALA A 157 -129.37 57.44 REMARK 500 HIS B 61 33.44 -94.59 REMARK 500 ARG B 79 -152.31 59.01 REMARK 500 ASN B 152 45.73 -93.15 REMARK 500 VAL B 181 -62.93 -99.08 REMARK 500 CYS C 41 -47.91 104.59 REMARK 500 HIS C 115 -40.11 71.89 REMARK 500 THR C 144 -165.10 -103.70 REMARK 500 ALA C 157 -130.54 57.35 REMARK 500 HIS D 61 33.20 -94.65 REMARK 500 GLU D 77 74.46 -69.92 REMARK 500 PHE D 80 2.08 -67.73 REMARK 500 ASN D 152 45.51 -93.75 REMARK 500 VAL D 181 -62.79 -99.53 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL C 201 DBREF 5WYH A 2 182 UNP Q9UBQ0 VPS29_HUMAN 2 182 DBREF 5WYH B 3 200 UNP G8UZ99 G8UZ99_LEGPN 3 200 DBREF 5WYH C 2 182 UNP Q9UBQ0 VPS29_HUMAN 2 182 DBREF 5WYH D 3 200 UNP G8UZ99 G8UZ99_LEGPN 3 200 SEQADV 5WYH ALA A -2 UNP Q9UBQ0 EXPRESSION TAG SEQADV 5WYH GLY A -1 UNP Q9UBQ0 EXPRESSION TAG SEQADV 5WYH HIS A 0 UNP Q9UBQ0 EXPRESSION TAG SEQADV 5WYH ARG A 1 UNP Q9UBQ0 EXPRESSION TAG SEQADV 5WYH ALA C -2 UNP Q9UBQ0 EXPRESSION TAG SEQADV 5WYH GLY C -1 UNP Q9UBQ0 EXPRESSION TAG SEQADV 5WYH HIS C 0 UNP Q9UBQ0 EXPRESSION TAG SEQADV 5WYH ARG C 1 UNP Q9UBQ0 EXPRESSION TAG SEQRES 1 A 185 ALA GLY HIS ARG LEU VAL LEU VAL LEU GLY ASP LEU HIS SEQRES 2 A 185 ILE PRO HIS ARG CYS ASN SER LEU PRO ALA LYS PHE LYS SEQRES 3 A 185 LYS LEU LEU VAL PRO GLY LYS ILE GLN HIS ILE LEU CYS SEQRES 4 A 185 THR GLY ASN LEU CYS THR LYS GLU SER TYR ASP TYR LEU SEQRES 5 A 185 LYS THR LEU ALA GLY ASP VAL HIS ILE VAL ARG GLY ASP SEQRES 6 A 185 PHE ASP GLU ASN LEU ASN TYR PRO GLU GLN LYS VAL VAL SEQRES 7 A 185 THR VAL GLY GLN PHE LYS ILE GLY LEU ILE HIS GLY HIS SEQRES 8 A 185 GLN VAL ILE PRO TRP GLY ASP MET ALA SER LEU ALA LEU SEQRES 9 A 185 LEU GLN ARG GLN PHE ASP VAL ASP ILE LEU ILE SER GLY SEQRES 10 A 185 HIS THR HIS LYS PHE GLU ALA PHE GLU HIS GLU ASN LYS SEQRES 11 A 185 PHE TYR ILE ASN PRO GLY SER ALA THR GLY ALA TYR ASN SEQRES 12 A 185 ALA LEU GLU THR ASN ILE ILE PRO SER PHE VAL LEU MET SEQRES 13 A 185 ASP ILE GLN ALA SER THR VAL VAL THR TYR VAL TYR GLN SEQRES 14 A 185 LEU ILE GLY ASP ASP VAL LYS VAL GLU ARG ILE GLU TYR SEQRES 15 A 185 LYS LYS PRO SEQRES 1 B 198 LEU GLU GLU TYR ILE ARG MET ALA LYS ASN LYS GLU PHE SEQRES 2 B 198 PHE ASP ALA LEU GLU GLU ILE ALA GLU SER ALA LYS ASN SEQRES 3 B 198 ASP GLU THR LEU ARG ASN GLU LEU ALA LYS VAL LEU ASP SEQRES 4 B 198 ASP ILE LEU LYS THR ASP PRO SER ASP PRO GLU ALA PHE SEQRES 5 B 198 ARG LYS ILE VAL ALA GLU HIS GLN GLU PHE TRP ASP GLU SEQRES 6 B 198 HIS ASP PRO SER LEU MET GLU PHE ASN GLU GLY ARG PHE SEQRES 7 B 198 PHE GLY LYS SER ARG LYS GLN TYR LEU LYS SER ASP ASP SEQRES 8 B 198 PHE LEU ASN SER THR ASP PRO THR TYR ASN PHE GLN LYS SEQRES 9 B 198 LEU HIS GLN PHE ALA ALA GLU GLN ARG VAL LYS LEU GLY SEQRES 10 B 198 LEU GLU LYS SER ASP THR ASP THR LEU VAL ALA ILE LEU SEQRES 11 B 198 LYS ASN ASN PRO GLU GLU CYS ARG ALA TYR ILE GLU SER SEQRES 12 B 198 LYS LYS PRO GLY LEU GLY ASN PHE SER GLU GLY ASN VAL SEQRES 13 B 198 HIS GLY TRP LEU LYS GLU GLU TYR THR PRO THR ILE PRO SEQRES 14 B 198 PRO LYS ALA ILE ASN LYS SER THR GLY VAL LEU SER ASP SEQRES 15 B 198 GLU ALA ILE LYS ARG ILE LYS GLU GLN ALA ARG ASP LEU SEQRES 16 B 198 LEU LEU LEU SEQRES 1 C 185 ALA GLY HIS ARG LEU VAL LEU VAL LEU GLY ASP LEU HIS SEQRES 2 C 185 ILE PRO HIS ARG CYS ASN SER LEU PRO ALA LYS PHE LYS SEQRES 3 C 185 LYS LEU LEU VAL PRO GLY LYS ILE GLN HIS ILE LEU CYS SEQRES 4 C 185 THR GLY ASN LEU CYS THR LYS GLU SER TYR ASP TYR LEU SEQRES 5 C 185 LYS THR LEU ALA GLY ASP VAL HIS ILE VAL ARG GLY ASP SEQRES 6 C 185 PHE ASP GLU ASN LEU ASN TYR PRO GLU GLN LYS VAL VAL SEQRES 7 C 185 THR VAL GLY GLN PHE LYS ILE GLY LEU ILE HIS GLY HIS SEQRES 8 C 185 GLN VAL ILE PRO TRP GLY ASP MET ALA SER LEU ALA LEU SEQRES 9 C 185 LEU GLN ARG GLN PHE ASP VAL ASP ILE LEU ILE SER GLY SEQRES 10 C 185 HIS THR HIS LYS PHE GLU ALA PHE GLU HIS GLU ASN LYS SEQRES 11 C 185 PHE TYR ILE ASN PRO GLY SER ALA THR GLY ALA TYR ASN SEQRES 12 C 185 ALA LEU GLU THR ASN ILE ILE PRO SER PHE VAL LEU MET SEQRES 13 C 185 ASP ILE GLN ALA SER THR VAL VAL THR TYR VAL TYR GLN SEQRES 14 C 185 LEU ILE GLY ASP ASP VAL LYS VAL GLU ARG ILE GLU TYR SEQRES 15 C 185 LYS LYS PRO SEQRES 1 D 198 LEU GLU GLU TYR ILE ARG MET ALA LYS ASN LYS GLU PHE SEQRES 2 D 198 PHE ASP ALA LEU GLU GLU ILE ALA GLU SER ALA LYS ASN SEQRES 3 D 198 ASP GLU THR LEU ARG ASN GLU LEU ALA LYS VAL LEU ASP SEQRES 4 D 198 ASP ILE LEU LYS THR ASP PRO SER ASP PRO GLU ALA PHE SEQRES 5 D 198 ARG LYS ILE VAL ALA GLU HIS GLN GLU PHE TRP ASP GLU SEQRES 6 D 198 HIS ASP PRO SER LEU MET GLU PHE ASN GLU GLY ARG PHE SEQRES 7 D 198 PHE GLY LYS SER ARG LYS GLN TYR LEU LYS SER ASP ASP SEQRES 8 D 198 PHE LEU ASN SER THR ASP PRO THR TYR ASN PHE GLN LYS SEQRES 9 D 198 LEU HIS GLN PHE ALA ALA GLU GLN ARG VAL LYS LEU GLY SEQRES 10 D 198 LEU GLU LYS SER ASP THR ASP THR LEU VAL ALA ILE LEU SEQRES 11 D 198 LYS ASN ASN PRO GLU GLU CYS ARG ALA TYR ILE GLU SER SEQRES 12 D 198 LYS LYS PRO GLY LEU GLY ASN PHE SER GLU GLY ASN VAL SEQRES 13 D 198 HIS GLY TRP LEU LYS GLU GLU TYR THR PRO THR ILE PRO SEQRES 14 D 198 PRO LYS ALA ILE ASN LYS SER THR GLY VAL LEU SER ASP SEQRES 15 D 198 GLU ALA ILE LYS ARG ILE LYS GLU GLN ALA ARG ASP LEU SEQRES 16 D 198 LEU LEU LEU HET GOL C 201 6 HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 5 GOL C3 H8 O3 FORMUL 6 HOH *226(H2 O) HELIX 1 AA1 PRO A 19 LEU A 26 1 8 HELIX 2 AA2 THR A 42 ALA A 53 1 12 HELIX 3 AA3 ASP A 95 ASP A 107 1 13 HELIX 4 AA4 LYS B 11 LYS B 27 1 17 HELIX 5 AA5 ASP B 29 THR B 46 1 18 HELIX 6 AA6 ASP B 50 HIS B 61 1 12 HELIX 7 AA7 HIS B 61 ASP B 69 1 9 HELIX 8 AA8 SER B 84 LYS B 90 1 7 HELIX 9 AA9 ASN B 103 GLU B 121 1 19 HELIX 10 AB1 ASP B 124 ASN B 134 1 11 HELIX 11 AB2 ASN B 135 LYS B 146 1 12 HELIX 12 AB3 SER B 183 LEU B 200 1 18 HELIX 13 AB4 PRO C 19 LEU C 26 1 8 HELIX 14 AB5 THR C 42 ALA C 53 1 12 HELIX 15 AB6 ASP C 95 ASP C 107 1 13 HELIX 16 AB7 LYS D 11 LYS D 27 1 17 HELIX 17 AB8 ASP D 29 THR D 46 1 18 HELIX 18 AB9 ASP D 50 HIS D 61 1 12 HELIX 19 AC1 HIS D 61 ASP D 69 1 9 HELIX 20 AC2 SER D 84 LYS D 90 1 7 HELIX 21 AC3 ASN D 103 GLU D 121 1 19 HELIX 22 AC4 ASP D 124 ASN D 134 1 11 HELIX 23 AC5 ASN D 135 LYS D 146 1 12 HELIX 24 AC6 SER D 183 LEU D 199 1 17 SHEET 1 AA1 6 ASP A 55 ILE A 58 0 SHEET 2 AA1 6 HIS A 33 CYS A 36 1 N ILE A 34 O HIS A 57 SHEET 3 AA1 6 ARG A 1 LEU A 6 1 N LEU A 4 O LEU A 35 SHEET 4 AA1 6 SER A 149 GLN A 156 -1 O VAL A 151 N VAL A 5 SHEET 5 AA1 6 THR A 159 ILE A 168 -1 O VAL A 161 N ASP A 154 SHEET 6 AA1 6 ASP A 171 LYS A 180 -1 O ILE A 177 N THR A 162 SHEET 1 AA2 5 GLN A 72 VAL A 77 0 SHEET 2 AA2 5 PHE A 80 ILE A 85 -1 O ILE A 82 N VAL A 75 SHEET 3 AA2 5 ILE A 110 SER A 113 1 O ILE A 112 N GLY A 83 SHEET 4 AA2 5 LYS A 127 ASN A 131 1 O ILE A 130 N LEU A 111 SHEET 5 AA2 5 GLU A 120 HIS A 124 -1 N GLU A 120 O ASN A 131 SHEET 1 AA3 2 GLU B 165 TYR B 166 0 SHEET 2 AA3 2 ALA B 174 ILE B 175 -1 O ILE B 175 N GLU B 165 SHEET 1 AA4 6 ASP C 55 ILE C 58 0 SHEET 2 AA4 6 HIS C 33 CYS C 36 1 N ILE C 34 O HIS C 57 SHEET 3 AA4 6 ARG C 1 LEU C 6 1 N LEU C 4 O LEU C 35 SHEET 4 AA4 6 SER C 149 GLN C 156 -1 O VAL C 151 N VAL C 5 SHEET 5 AA4 6 THR C 159 ILE C 168 -1 O VAL C 161 N ASP C 154 SHEET 6 AA4 6 ASP C 171 LYS C 180 -1 O ILE C 177 N THR C 162 SHEET 1 AA5 5 GLN C 72 VAL C 77 0 SHEET 2 AA5 5 PHE C 80 ILE C 85 -1 O ILE C 82 N VAL C 75 SHEET 3 AA5 5 ILE C 110 SER C 113 1 O ILE C 112 N GLY C 83 SHEET 4 AA5 5 LYS C 127 ASN C 131 1 O ILE C 130 N LEU C 111 SHEET 5 AA5 5 GLU C 120 HIS C 124 -1 N GLU C 120 O ASN C 131 SHEET 1 AA6 2 GLU D 165 TYR D 166 0 SHEET 2 AA6 2 ALA D 174 ILE D 175 -1 O ILE D 175 N GLU D 165 CISPEP 1 ILE A 11 PRO A 12 0 8.18 CISPEP 2 ILE A 91 PRO A 92 0 -2.89 CISPEP 3 LYS B 147 PRO B 148 0 -0.26 CISPEP 4 ILE B 170 PRO B 171 0 -14.27 CISPEP 5 ILE C 11 PRO C 12 0 7.76 CISPEP 6 ILE C 91 PRO C 92 0 -2.78 CISPEP 7 LYS D 147 PRO D 148 0 -0.63 CISPEP 8 ILE D 170 PRO D 171 0 -12.82 SITE 1 AC1 6 TYR C 46 VAL C 56 ILE C 58 LYS C 73 SITE 2 AC1 6 HOH C 315 HOH C 361 CRYST1 44.312 82.049 87.332 101.73 104.26 104.77 P 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 0.022567 0.005948 0.007744 0.00000 SCALE2 0.000000 0.012604 0.003732 0.00000 SCALE3 0.000000 0.000000 0.012322 0.00000