PDB Short entry for 3WHT HEADER PROTEIN TRANSPORT 30-AUG-13 3WHT TITLE CRYSTAL STRUCTURE OF ERGIC-53/MCFD2, CALCIUM-FREE FORM COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN ERGIC-53; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: CARBOHYDRATE RECOGNITION DOMAIN (UNP RESIDUES 31-269); COMPND 5 SYNONYM: ER-GOLGI INTERMEDIATE COMPARTMENT 53 KDA PROTEIN, GP58, COMPND 6 INTRACELLULAR MANNOSE-SPECIFIC LECTIN MR60, LECTIN MANNOSE-BINDING 1; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: MULTIPLE COAGULATION FACTOR DEFICIENCY PROTEIN 2; COMPND 10 CHAIN: B; COMPND 11 FRAGMENT: UNP RESIDUES 67-146; COMPND 12 SYNONYM: NEURAL STEM CELL-DERIVED NEURONAL SURVIVAL PROTEIN; COMPND 13 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: ERGIC53; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21-CODONPLUS(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PCOLD-III; SOURCE 11 MOL_ID: 2; SOURCE 12 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 13 ORGANISM_COMMON: HUMAN; SOURCE 14 ORGANISM_TAXID: 9606; SOURCE 15 GENE: MCFD2; SOURCE 16 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 17 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 18 EXPRESSION_SYSTEM_STRAIN: BL21-CODONPLUS(DE3); SOURCE 19 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 20 EXPRESSION_SYSTEM_PLASMID: PET-16B KEYWDS BETA-SANDWICH, EF-HAND, CARGO RECEPTOR, CALCIUM BINDING, ER, ERGIC, KEYWDS 2 PROTEIN TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR T.SATOH,K.SUZUKI,K.KATO REVDAT 3 08-NOV-23 3WHT 1 REMARK SEQADV LINK REVDAT 2 19-FEB-14 3WHT 1 JRNL REVDAT 1 15-JAN-14 3WHT 0 JRNL AUTH T.SATOH,K.SUZUKI,T.YAMAGUCHI,K.KATO JRNL TITL STRUCTURAL BASIS FOR DISPARATE SUGAR-BINDING SPECIFICITIES JRNL TITL 2 IN THE HOMOLOGOUS CARGO RECEPTORS ERGIC-53 AND VIP36 JRNL REF PLOS ONE V. 9 87963 2014 JRNL REFN ESSN 1932-6203 JRNL PMID 24498414 JRNL DOI 10.1371/JOURNAL.PONE.0087963 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.7.0029 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 96.6 REMARK 3 NUMBER OF REFLECTIONS : 27848 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) : 0.177 REMARK 3 R VALUE (WORKING SET) : 0.175 REMARK 3 FREE R VALUE : 0.202 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1484 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) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.85 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1953 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 91.00 REMARK 3 BIN R VALUE (WORKING SET) : 0.2440 REMARK 3 BIN FREE R VALUE SET COUNT : 90 REMARK 3 BIN FREE R VALUE : 0.2560 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2128 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 15 REMARK 3 SOLVENT ATOMS : 195 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 17.10 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 24.17 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.08000 REMARK 3 B22 (A**2) : -0.25000 REMARK 3 B33 (A**2) : -0.73000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.01000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.116 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.108 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.069 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.201 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.956 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.937 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2193 ; 0.012 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 2019 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2968 ; 1.491 ; 1.932 REMARK 3 BOND ANGLES OTHERS (DEGREES): 4626 ; 0.773 ; 3.001 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 266 ; 6.438 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 114 ;30.690 ;24.561 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 343 ;12.886 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 11 ;14.976 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 315 ; 0.097 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2529 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 544 ; 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL 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 : NULL 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 : 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 3WHT COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 13-SEP-13. REMARK 100 THE DEPOSITION ID IS D_1000096352. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-FEB-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : AR-NE3A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00000 REMARK 200 MONOCHROMATOR : SI 111 REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 270 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 29334 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 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 (%) : 97.0 REMARK 200 DATA REDUNDANCY : 3.800 REMARK 200 R MERGE (I) : 0.07700 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 26.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.83 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.7 REMARK 200 DATA REDUNDANCY IN SHELL : 3.90 REMARK 200 R MERGE FOR SHELL (I) : 0.43400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 4.100 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: 3A4U REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.67 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.11 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG5000 MONOMETHYL ETHER, 100MM REMARK 280 BIS-TRIS, PH 6.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 289K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z REMARK 290 4555 -X+1/2,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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 51.99500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 29.88000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 51.99500 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 29.88000 REMARK 290 SMTRY3 4 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2490 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12540 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -46.0 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 535 LIES ON A SPECIAL POSITION. 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 MET A 24 REMARK 465 ASN A 25 REMARK 465 HIS A 26 REMARK 465 LYS A 27 REMARK 465 VAL A 28 REMARK 465 HIS A 29 REMARK 465 MET A 30 REMARK 465 ASP A 31 REMARK 465 GLY A 32 REMARK 465 VAL A 33 REMARK 465 GLY A 34 REMARK 465 GLY A 35 REMARK 465 ASP A 36 REMARK 465 PRO A 37 REMARK 465 ALA A 38 REMARK 465 VAL A 39 REMARK 465 ALA A 40 REMARK 465 LEU A 41 REMARK 465 PRO A 42 REMARK 465 HIS A 43 REMARK 465 ASP A 155 REMARK 465 ASN A 156 REMARK 465 ASP A 157 REMARK 465 GLY A 158 REMARK 465 LYS A 159 REMARK 465 LYS A 160 REMARK 465 ASN A 161 REMARK 465 TYR A 176 REMARK 465 ASP A 177 REMARK 465 HIS A 178 REMARK 465 GLN A 179 REMARK 465 ASN A 180 REMARK 465 ASP A 181 REMARK 465 GLY A 182 REMARK 465 ALA A 183 REMARK 465 SER A 184 REMARK 465 GLN A 185 REMARK 465 GLU A 269 REMARK 465 MET B 43 REMARK 465 GLY B 44 REMARK 465 HIS B 45 REMARK 465 HIS B 46 REMARK 465 HIS B 47 REMARK 465 HIS B 48 REMARK 465 HIS B 49 REMARK 465 HIS B 50 REMARK 465 HIS B 51 REMARK 465 HIS B 52 REMARK 465 HIS B 53 REMARK 465 HIS B 54 REMARK 465 SER B 55 REMARK 465 SER B 56 REMARK 465 GLY B 57 REMARK 465 HIS B 58 REMARK 465 ILE B 59 REMARK 465 GLU B 60 REMARK 465 GLY B 61 REMARK 465 ARG B 62 REMARK 465 HIS B 63 REMARK 465 MET B 64 REMARK 465 LEU B 65 REMARK 465 GLU B 66 REMARK 465 MET B 67 REMARK 465 SER B 68 REMARK 465 PRO B 69 REMARK 465 THR B 98 REMARK 465 HIS B 99 REMARK 465 VAL B 100 REMARK 465 HIS B 101 REMARK 465 LYS B 102 REMARK 465 GLU B 103 REMARK 465 GLU B 104 REMARK 465 GLY B 105 REMARK 465 SER B 106 REMARK 465 GLU B 107 REMARK 465 GLN B 108 REMARK 465 ALA B 109 REMARK 465 PRO B 110 REMARK 465 SER B 144 REMARK 465 LEU B 145 REMARK 465 GLN B 146 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 PHE A 66 -2.21 79.31 REMARK 500 ASN A 72 32.42 -98.86 REMARK 500 ALA A 100 74.88 -118.65 REMARK 500 GLN A 173 15.82 -143.14 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 B 501 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 81 OD1 REMARK 620 2 ASP B 83 OD1 81.3 REMARK 620 3 ASN B 85 OD1 84.2 76.1 REMARK 620 4 LEU B 87 O 87.0 152.8 78.4 REMARK 620 5 GLU B 92 OE2 96.8 80.1 155.8 125.8 REMARK 620 6 GLU B 92 OE1 117.7 129.7 146.1 77.4 53.1 REMARK 620 7 HOH B 602 O 161.2 82.3 83.0 103.8 89.4 80.2 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA B 502 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 129 OD1 REMARK 620 2 ASN B 131 OD1 83.1 REMARK 620 3 ASP B 133 OD1 87.6 75.9 REMARK 620 4 TYR B 135 O 78.3 153.3 84.3 REMARK 620 5 HOH B 606 O 162.2 84.9 76.7 108.0 REMARK 620 6 HOH B 622 O 95.0 70.8 146.1 129.4 93.4 REMARK 620 7 HOH B 659 O 144.0 124.1 119.5 81.2 53.6 75.8 REMARK 620 N 1 2 3 4 5 6 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA B 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA B 502 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3A4U RELATED DB: PDB REMARK 900 RELATED ID: 1GV9 RELATED DB: PDB REMARK 900 RELATED ID: 1R1Z RELATED DB: PDB REMARK 900 RELATED ID: 4GKY RELATED DB: PDB REMARK 900 RELATED ID: 4GKX RELATED DB: PDB REMARK 900 RELATED ID: 3LCP RELATED DB: PDB REMARK 900 RELATED ID: 3WHU RELATED DB: PDB DBREF 3WHT A 31 269 UNP P49257 LMAN1_HUMAN 31 269 DBREF 3WHT B 67 146 UNP Q8NI22 MCFD2_HUMAN 67 146 SEQADV 3WHT MET A 24 UNP P49257 EXPRESSION TAG SEQADV 3WHT ASN A 25 UNP P49257 EXPRESSION TAG SEQADV 3WHT HIS A 26 UNP P49257 EXPRESSION TAG SEQADV 3WHT LYS A 27 UNP P49257 EXPRESSION TAG SEQADV 3WHT VAL A 28 UNP P49257 EXPRESSION TAG SEQADV 3WHT HIS A 29 UNP P49257 EXPRESSION TAG SEQADV 3WHT MET A 30 UNP P49257 EXPRESSION TAG SEQADV 3WHT MET B 43 UNP Q8NI22 EXPRESSION TAG SEQADV 3WHT GLY B 44 UNP Q8NI22 EXPRESSION TAG SEQADV 3WHT HIS B 45 UNP Q8NI22 EXPRESSION TAG SEQADV 3WHT HIS B 46 UNP Q8NI22 EXPRESSION TAG SEQADV 3WHT HIS B 47 UNP Q8NI22 EXPRESSION TAG SEQADV 3WHT HIS B 48 UNP Q8NI22 EXPRESSION TAG SEQADV 3WHT HIS B 49 UNP Q8NI22 EXPRESSION TAG SEQADV 3WHT HIS B 50 UNP Q8NI22 EXPRESSION TAG SEQADV 3WHT HIS B 51 UNP Q8NI22 EXPRESSION TAG SEQADV 3WHT HIS B 52 UNP Q8NI22 EXPRESSION TAG SEQADV 3WHT HIS B 53 UNP Q8NI22 EXPRESSION TAG SEQADV 3WHT HIS B 54 UNP Q8NI22 EXPRESSION TAG SEQADV 3WHT SER B 55 UNP Q8NI22 EXPRESSION TAG SEQADV 3WHT SER B 56 UNP Q8NI22 EXPRESSION TAG SEQADV 3WHT GLY B 57 UNP Q8NI22 EXPRESSION TAG SEQADV 3WHT HIS B 58 UNP Q8NI22 EXPRESSION TAG SEQADV 3WHT ILE B 59 UNP Q8NI22 EXPRESSION TAG SEQADV 3WHT GLU B 60 UNP Q8NI22 EXPRESSION TAG SEQADV 3WHT GLY B 61 UNP Q8NI22 EXPRESSION TAG SEQADV 3WHT ARG B 62 UNP Q8NI22 EXPRESSION TAG SEQADV 3WHT HIS B 63 UNP Q8NI22 EXPRESSION TAG SEQADV 3WHT MET B 64 UNP Q8NI22 EXPRESSION TAG SEQADV 3WHT LEU B 65 UNP Q8NI22 EXPRESSION TAG SEQADV 3WHT GLU B 66 UNP Q8NI22 EXPRESSION TAG SEQRES 1 A 246 MET ASN HIS LYS VAL HIS MET ASP GLY VAL GLY GLY ASP SEQRES 2 A 246 PRO ALA VAL ALA LEU PRO HIS ARG ARG PHE GLU TYR LYS SEQRES 3 A 246 TYR SER PHE LYS GLY PRO HIS LEU VAL GLN SER ASP GLY SEQRES 4 A 246 THR VAL PRO PHE TRP ALA HIS ALA GLY ASN ALA ILE PRO SEQRES 5 A 246 SER SER ASP GLN ILE ARG VAL ALA PRO SER LEU LYS SER SEQRES 6 A 246 GLN ARG GLY SER VAL TRP THR LYS THR LYS ALA ALA PHE SEQRES 7 A 246 GLU ASN TRP GLU VAL GLU VAL THR PHE ARG VAL THR GLY SEQRES 8 A 246 ARG GLY ARG ILE GLY ALA ASP GLY LEU ALA ILE TRP TYR SEQRES 9 A 246 ALA GLU ASN GLN GLY LEU GLU GLY PRO VAL PHE GLY SER SEQRES 10 A 246 ALA ASP LEU TRP ASN GLY VAL GLY ILE PHE PHE ASP SER SEQRES 11 A 246 PHE ASP ASN ASP GLY LYS LYS ASN ASN PRO ALA ILE VAL SEQRES 12 A 246 ILE ILE GLY ASN ASN GLY GLN ILE HIS TYR ASP HIS GLN SEQRES 13 A 246 ASN ASP GLY ALA SER GLN ALA LEU ALA SER CYS GLN ARG SEQRES 14 A 246 ASP PHE ARG ASN LYS PRO TYR PRO VAL ARG ALA LYS ILE SEQRES 15 A 246 THR TYR TYR GLN ASN THR LEU THR VAL MET ILE ASN ASN SEQRES 16 A 246 GLY PHE THR PRO ASP LYS ASN ASP TYR GLU PHE CYS ALA SEQRES 17 A 246 LYS VAL GLU ASN MET ILE ILE PRO ALA GLN GLY HIS PHE SEQRES 18 A 246 GLY ILE SER ALA ALA THR GLY GLY LEU ALA ASP ASP HIS SEQRES 19 A 246 ASP VAL LEU SER PHE LEU THR PHE GLN LEU THR GLU SEQRES 1 B 104 MET GLY HIS HIS HIS HIS HIS HIS HIS HIS HIS HIS SER SEQRES 2 B 104 SER GLY HIS ILE GLU GLY ARG HIS MET LEU GLU MET SER SEQRES 3 B 104 PRO GLN GLU LEU GLN LEU HIS TYR PHE LYS MET HIS ASP SEQRES 4 B 104 TYR ASP GLY ASN ASN LEU LEU ASP GLY LEU GLU LEU SER SEQRES 5 B 104 THR ALA ILE THR HIS VAL HIS LYS GLU GLU GLY SER GLU SEQRES 6 B 104 GLN ALA PRO LEU MET SER GLU ASP GLU LEU ILE ASN ILE SEQRES 7 B 104 ILE ASP GLY VAL LEU ARG ASP ASP ASP LYS ASN ASN ASP SEQRES 8 B 104 GLY TYR ILE ASP TYR ALA GLU PHE ALA LYS SER LEU GLN HET CL A 301 1 HET GOL A 302 6 HET GOL A 303 6 HET CA B 501 1 HET CA B 502 1 HETNAM CL CHLORIDE ION HETNAM GOL GLYCEROL HETNAM CA CALCIUM ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 CL CL 1- FORMUL 4 GOL 2(C3 H8 O3) FORMUL 6 CA 2(CA 2+) FORMUL 8 HOH *195(H2 O) HELIX 1 1 TYR A 48 SER A 51 5 4 HELIX 2 2 GLU B 71 HIS B 80 1 10 HELIX 3 3 ASP B 89 ALA B 96 1 8 HELIX 4 4 SER B 113 ASP B 129 1 17 HELIX 5 5 ASP B 137 LYS B 143 1 7 SHEET 1 A 4 ARG A 45 PHE A 46 0 SHEET 2 A 4 ASP A 256 GLN A 266 -1 O GLN A 266 N ARG A 45 SHEET 3 A 4 ILE A 80 ALA A 83 -1 N ILE A 80 O VAL A 259 SHEET 4 A 4 ILE A 74 PRO A 75 -1 N ILE A 74 O ARG A 81 SHEET 1 B 6 PHE A 52 LYS A 53 0 SHEET 2 B 6 ASP A 256 GLN A 266 -1 O PHE A 262 N PHE A 52 SHEET 3 B 6 TRP A 104 THR A 113 -1 N ARG A 111 O ASP A 258 SHEET 4 B 6 VAL A 201 TYR A 208 -1 O TYR A 207 N TRP A 104 SHEET 5 B 6 THR A 211 ASN A 217 -1 O MET A 215 N LYS A 204 SHEET 6 B 6 GLU A 228 VAL A 233 -1 O GLU A 228 N ILE A 216 SHEET 1 C 7 TRP A 67 GLY A 71 0 SHEET 2 C 7 ARG A 90 THR A 95 -1 O TRP A 94 N ALA A 68 SHEET 3 C 7 HIS A 243 ALA A 249 -1 O PHE A 244 N THR A 95 SHEET 4 C 7 GLY A 122 ALA A 128 -1 N ALA A 128 O HIS A 243 SHEET 5 C 7 ASN A 145 ASP A 152 -1 O PHE A 151 N LEU A 123 SHEET 6 C 7 ALA A 164 ASN A 171 -1 O VAL A 166 N PHE A 150 SHEET 7 C 7 ALA A 188 GLN A 191 -1 O CYS A 190 N ILE A 165 SSBOND 1 CYS A 190 CYS A 230 1555 1555 2.06 LINK OD1 ASP B 81 CA CA B 501 1555 1555 2.29 LINK OD1 ASP B 83 CA CA B 501 1555 1555 2.38 LINK OD1 ASN B 85 CA CA B 501 1555 1555 2.39 LINK O LEU B 87 CA CA B 501 1555 1555 2.27 LINK OE2 GLU B 92 CA CA B 501 1555 1555 2.43 LINK OE1 GLU B 92 CA CA B 501 1555 1555 2.53 LINK OD1 ASP B 129 CA CA B 502 1555 1555 2.30 LINK OD1 ASN B 131 CA CA B 502 1555 1555 2.39 LINK OD1 ASP B 133 CA CA B 502 1555 1555 2.44 LINK O TYR B 135 CA CA B 502 1555 1555 2.38 LINK CA CA B 501 O HOH B 602 1555 1555 2.51 LINK CA CA B 502 O HOH B 606 1555 1555 2.69 LINK CA CA B 502 O HOH B 622 1555 1555 2.35 LINK CA CA B 502 O HOH B 659 1555 1555 2.66 CISPEP 1 GLY A 54 PRO A 55 0 0.90 CISPEP 2 ALA A 120 ASP A 121 0 -10.24 CISPEP 3 ASN A 162 PRO A 163 0 -1.74 SITE 1 AC1 2 LYS A 53 TYR B 135 SITE 1 AC2 9 LYS A 53 GLY A 54 PRO A 55 HIS A 56 SITE 2 AC2 9 LEU A 57 HOH A 403 TYR B 82 LEU B 91 SITE 3 AC2 9 HOH B 604 SITE 1 AC3 8 PHE A 101 GLU A 102 TRP A 104 TYR A 127 SITE 2 AC3 8 TYR A 207 ILE A 238 PRO A 239 ALA A 240 SITE 1 AC4 6 ASP B 81 ASP B 83 ASN B 85 LEU B 87 SITE 2 AC4 6 GLU B 92 HOH B 602 SITE 1 AC5 7 ASP B 129 ASN B 131 ASP B 133 TYR B 135 SITE 2 AC5 7 HOH B 606 HOH B 622 HOH B 659 CRYST1 103.990 59.760 55.070 90.00 104.90 90.00 C 1 2 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 0.009616 0.000000 0.002558 0.00000 SCALE2 0.000000 0.016735 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018790 0.00000